One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020)

Napalai Chaiwan

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.

Fungal Diversity (2020) 103:87–218 https://doi.org/10.1007/s13225-020-00460-8 One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020) Ruvishika S. Jayawardena1,2,7 · Kevin D. Hyde1,2,3,18 · Yi Jyun Chen2,7 · Viktor Papp4 · Balázs Palla4 · Dávid Papp5,6 · Chitrabhanu S. Bhunjun2,7 · Vedprakash G. Hurdeal2,7 · Chanokned Senwanna2,8 · Ishara S. Manawasinghe2,9,18 · Dulanjalee L. Harischandra2,7,9 · Ajay Kumar Gautam10 · Shubhi Avasthi11 · Boontiya Chuankid2,7 · Ishani D. Goonasekara2,7 · Sinang Hongsanan12 · XiangYu Zeng2,7,19 · Kapila K. Liyanage2,17,20 · NingGuo Liu2 · Anuruddha Karunarathna2,8 · Kalani K. Hapuarachchi2 · Thatsanee Luangharn2,3 · Olivier Raspé2,7 · Rashika Brahmanage2,7,9 · Mingkwan Doilom3,16,17 · Hyang B. Lee13 · Liu Mei9 · Rajesh Jeewon14 · Naruemon Huanraluek2 · Napalai Chaiwan2,7 · Marc Stadler15 · Yong Wang1 Received: 20 May 2020 / Accepted: 7 August 2020 / Published online: 24 September 2020 © The Author(s) 2020 Abstract This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described. Keywords Disease · Plant pathology · Phylogeny · Taxonomy · Symptoms Contents and contributors (main contributors underlined) Newly discussed genera and family 76. 77. 78. 79. 80. 81. 82. 83. 84. 85. 86. 87. Armillaria – B Chuankid, M Stadler Barriopsis – IS Manawasinghe, RS Jayawardena Cercospora – ID Goonasekara Clinoconidium – AK Gautam, S Avasthi Cylindrocladiella – D Harischandra, RS Jayawardena Dothidotthia – C Senwanna Erysiphaceae – KK Liyanage, RS Jayawardena, KD Hyde Fomitopsis – V Papp, B Palla, D Papp Ganoderma – KK Hapuarachchi, T Luangharn, O Raspe Golovinomyces – RS Jayawardena Heterobasidium – V Papp, B Palla, D Papp Meliola – S Hongsanan, XY Zeng 88. 89. 90. 91. 92. 93. 94. Neoerysiphe – RS Jayawardena Nothophoma – IS Manawasinghe, RS Jayawardena Phellinus – V Papp, B Palla, D Papp Pseudoseptoria – A Karunarathna, RS Jayawardena Stemphylium – RS Jayawardena, KD Hyde Thyrostroma – C Senwanna, KD Hyde Wojnowiciella – D Harischandra, RS Jayawardena Updated genera 95. 96. 97. 98. 99. 100. Cladosporium – NG Liu, RS Jayawardena Colletotrichum – RS Jayawardena, KD Hyde Mucor – VG Hurdeal, HB Lee Phytophthora – CS Bhunjun, RS Jayawardena Pythium – CS Bhunjun, RS Jayawardena Rhizopus – VG Hurdeal, HB Lee * Yong Wang yongwangbis@aliyun.com Extended author information available on the last page of the article 13 Vol.:(0123456789) 88 Fungal Diversity (2020) 103:87–218 Introduction This is the fourth paper in the One Stop Shop series focusing on providing a stable platform for the taxonomy of plant pathogenic fungi and fungus-like organisms. Genera included in this series are associated with plant diseases, and when the data are available we discuss the species that have been established as pathogens using Koch’s postulates. Some genera, however, are not well-known plant pathogens and some may be emerging pathogens, and need further studies to confirm their pathogenicity. Hyde et al. (2014) launched this series and stated its specific aims. Three issues of One Stop Shop (OSS) have been published treating 73 genera and two families of plant pathogenic fungi and fungus-like organisms (Hyde et al. 2014; Jayawardena et al. 2019a, b, Table 1). In this fourth contribution, a further 24 genera and one family are treated, providing clarification of their taxonomy and classification. Six of the entries are updates from previous entries as many changes have occurred in these genera. For each entry, the background of the genus, disease symptoms, host distribution, pathogen biology and epidemiology, morphological based identification, molecular-based identification, updated phylogeny and recommended genetic markers are provided and discussed. All contributed entries will be placed in the database, http://www.onestopshopfungi.org. The main outcome of this series is to enhance the current understanding of plant pathogens and gain better insights into the current classification, providing a stable taxonomy and phylogeny for plant pathogens. This will provide a definitive classification for mycologists and plant pathologists to accurately identify causal agents of disease and to implement accurate control strategies. Materials and methods Photo plates of the symptoms of the disease and morphological characters are given, when available. Classification follows Wijayawardene et al. (2020). For the treated taxa, all species that have been published until 30 March 2020 are included in the phylogenetic analyses. Sequence data from ex-type, ex-epitype or authentic or reference/voucher strains for each species were retrieved from GenBank. Sequence data from single gene regions Table 1 All entries treated in One stop shop (OSS) series OSS1 (Hyde et al. 2014) OSS2 (Jayawardena et al. 2019a) OSS3 (Jayawardena et al. 2019b) OSS4 (This paper) Bipolaris Botryosphaeriaceae Botryosphaeria Botrytis Choanephora Colletotrichum Curvularia Diaporthe Diplodia Dothiorella Fusarium Gilbertella Lasiodiplodia Mucor Neofusicoccum Pestalotiopsis Phyllosticta Phytophthora Puccinia Pyrenophora Pythium Rhizopus Stagonosporopsis Ustilago Verticillium Alternaria Bipolaris (update) Boeremia Botryosphaeria (update) Calonectria Coniella Corticiaceae Curvularia (update) Elsinoë Entyloma Erythricium Fomitiporia Fulviformes Laetisaria Limonomyces Neofabraea Neofusicoccum (update) Phaeoacremonium Phellinotus Phyllosticta (update) Plenodomus Pseudopyricularia Tilletia Venturia Waitea Alternaria (update) Capnodium Chaetothyrina Cytospora Cyphellophora Cyttaria Dactylonectria Diplodia (update) Dothiorella (update) Entoleuca Eutiarosporella Fusarium (update) Ilyonectria Lasiodiplodia (update) Macrophomina Medeolaria Neonectria Neopestalotiopsis Pestalotiopsis (update) Plasmopara Pseudopestalotiopsis Rosellinia Sphaeropsis Stagonosporopsis (update) Verticillium (update) Armillaria Barriopsis Cercospora Cladosporium (update) Clinoconidium Colletotrichum (update) Cylindricladiella Dothidotthia Erysiphaceae Fomitopsis Ganoderma Golovinomyces Heterobasidium Meliola Mucor (update) Neoerysiphe Nothophoma Phellinus Phytophthora (update) Pseudoseptoria Pythium (update) Rhizopus (update) Stemphylium Thyrostroma Wojnowiciella 13 Fungal Diversity (2020) 103:87–218 were aligned using Clustal Xv.1.81 (Thompson et al. 1997) and further alignment of the sequences carried out using the default settings of MAFFT v.7 (Katoh and Toh 2008; http://mafft.cbrc.jp/alignment/server/), and manual adjustment was conducted using BioEdit where necessary. Gene regions were also combined using BioEdit v.7.0.9.0 (Hall 1999). Primers for each gene locus can be found in the bibliography related to the phylogeny presented in each genus. Phylogenetic analyses consisted of maximum likelihood (ML), maximum parsimony (MP) and Bayesian posterior probability (BYPP). Maximum parsimony analysis was performed using PAUP (Phylogenetic Analysis Using Parsimony) v. 4.0b10 (Swofford 2002) to obtain the most parsimonious trees. Maximum likelihood analyses were also performed in raxmlGUIv.0.9b2 (Silvestro and Michalak 2010) or RAxML-HPC2 on XSEDE (8.2.8) on the CIPRES science gateway platform (http://www.phylo.org; Miller et al. 2010). Bayesian inference was conducted using MrBayes v. 3.2.6 on the CIPRES science gateway platform (http:// www.phylo.org; Miller et al. 2010) or stand-alone MrBayes v.3.1.2 (Ronquist and Huelsenbeck 2003). MrModeltest v. 2.3 (Nylander 2004) or jModeltest v. 2.1.4 (Darriba et al. 2012) was used for the statistical selection of the best-fit model of nucleotide substitution to parametrize the analyses. Results 76. Armillaria (Fr.) Staude, Schwämme Mitteldeutschl. 28: xxviii, 130 (1857) Background Armillaria is a plant pathogenic genus in the phylum Basidiomycota, family Physalacriaceae (He et al. 2019), collectively referred to as shoestring root-rot fungi or honey mushrooms. Armillaria can cause root-rot disease in a wide variety of woody hosts worldwide. Armillaria has undergone significant revision in the past 20 years. The genus once accommodated any white-spored agaric with broadly attached gills and an annulus (Volk et al. 1996). Armillaria mellea is the type species. Most Armillaria species have the potential to infect healthy and stressed trees, they differ in their pathogenicity to their hosts and under certain circumstances, they behave as obligate saprobes. Most Armillaria species are facultative necrotrophs causing root and butt rot on a broad range of woody plants affecting a variety of forest, shade, ornamental and orchard trees and shrubs. Some Armillaria species cause significant economic losses to forest trees and in nursery plantations. Armillaria root disease is found in many temperate and tropical forests throughout the world. This fungus spreads mainly through the interaction of tree roots. As saprotrophs, Armillaria species are important wood decomposers that contribute to nutrient 89 cycling in forest ecosystems. As pathogens, they infect and eventually kill susceptible trees, which impacts forest structure, composition and succession. Trees that are used for fibre or lumber production, as well as trees located in recreation sites, are affected by these diseases. Such Armillaria infections may cause yield reduction and tree mortality in silvicultural and agricultural tree plantations and provoke economic losses. Armillaria species are expected to become more aggressive during drought and thus enhance root rot (La Porta et al. 2008; Kolb et al. 2016; Kubiak et al. 2017). The incidence of Armillaria related root disease is likely to increase as temperatures increase and precipitation decreases due to climate change (Sturrock et al. 2011). Whilst the ability of the pathogen to sporulate, spread and infect is affected by temperature and moisture, factors that stress host trees directly may be just as critical to a successful invasion of host tissues. It seems likely that the disease will become more severe in the future, wherever Armillaria susceptible tree species are subjected to increased levels of climate stress (Klopfenstein et al. 2009). Currently, Armillaria root disease causes large growth/volume losses (e.g., 16–55%) in areas of western and North America (Filip and Goheen 1984; Cruickshank et al. 2011; Lockman and Kearns 2016). Armillaria root disease is typically more severe in trees that are maladapted to climateinduced stress (Ayres and Lombardero 2000; Kliejunas et al. 2009; Sturrock et al. 2011). Thus, it is likely that climate change will further exacerbate damage from Armillaria root disease, which can further predispose trees to beetle attack (e.g. Hertert et al. 1975; Tkacz and Schmitz 1986; Goheen and Hansen 1993). Armillaria mellea is an edible species that has long been used as a Traditional Chinese Medicine. Some of Armillaria species are is believed to be able to improve health and prevent various diseases, such as insomnia, pain, and neurasthenia. Extracts of A. mellea exhibit anti-oxidative, antiinflammatory and immune-modulatory activities. Armillaria mellea can also induce maturation of human dendritic cells. The chemical constituents isolated from A. mellea include sesquiterpenoids, steroids, triterpenoids, adenosine and resin acids. Armillariol C is a furan-based natural product isolated from Armillaria species. A xylosyl 1,3-galactofucan (AMPS-III) was isolated and identified as a novel antiinflammatory agent from this species. Classification—Basidiomycota, Agaricomycotina, Agaricomycetes, Agaricomycetidae, Agaricales, Physalacriaceae (He et al. 2019) Type species—Armillaria mellea (Vahl) P. Kumm. Distribution—Worldwide, mostly in temperate areas (northern and southern hemisphere) and some in tropical areas. Disease symptoms—Armillaria root disease, shoestring root rot 13 90 Symptoms caused by this fungus can be categorized into two categories: Crown symptoms—branch dieback, crown thinning, chlorosis, reddening of foliage or heavier than normal production of cones. Basal symptoms—the fungus can grow up from the roots in the inner bark in some tree species and causes basal cankers above the infected roots. Resinosis (exudation of resin) can be observed in resinous conifers. In some plants, decayed roots or decay in the inner wood of stem bases can be observed. Species cause a white rot of wood. In white rot, wood often has a bleached, whitish appearance and are spongy or stringy, and maybe wet. Black lines called “zone lines” are usually seen in the decayed wood. These lines are curved planes in the wood, sometimes called “pseudosclerotial plates”, composed of thickened, dark fungal cells. They may play a role in the protection of Armillaria from unfavourable conditions or other fungi that attempt to invade its territory, including other individuals of the same species. Actively decaying wood may be luminescent, producing a faint glow in the dark (Baumgartner and Rizzo 2002; Worrall 2004; Klopfenstein 2009). There are three major signs of Armillaria root disease in the field. Mycelial fans can always be seen in infected and recently killed trees. These are white mats of fungal mycelium between the inner bark and wood that are generally substantial and have a mushroom odour. Rhizomorphs are commonly associated with infection and are often attached to infected roots, but they may also be attached to the surface of uninfected roots. Depending on the species these may be few, small, fragile, hard to find or abundant and robust. Rhizomorphs can be cylindrical in soil or flattened under bark, reddish-brown to black branched and have a cream-coloured tip when actively growing (Guillaumin and Legrand 2013). Mushrooms that have honey-brown caps can be seen in clusters near or on the base of trees. Hosts—Many angiosperms and gymnosperms (especially conifers) in native, planted forests, orchards and vineyards (Farr and Rossman 2020). Pathogen biology, disease cycle and epidemiology Sexual reproduction results in the diploid mycelium. Such a mycelium is the dominant phase that is found growing in wood, growing through the soil as rhizomorphs, and killing trees. Armillaria species can be dispersed through airborne sexual basidiospores which will establish a new infection center. These taxa do not reproduce asexually but disperse by growing mycelium which is the most common source of infection, through root contacts or root grafts or by growing through the soil as rhizomorphs. Mycelium in colonized roots and the rhizomorphs produced serve as the 13 Fungal Diversity (2020) 103:87–218 most common mode of infection and may survive for up to 50 years or more in stumps, depending on the climate, size of the stump, and other factors (Baumgartner and Rizzo 2002; Worrall 2004; Klopfenstein 2009). Morphology-based identification and diversity Armillaria has included only white-spored wood-inhabiting agarics with broadly attached to decurrent gills and macroscopic black to reddish-brown rhizomorphs. Armillaria basidiomes are easily recognized by their caespitose habit, annulus and honey colour. It is, however, extremely difficult to identify some species due to the lack of morphological apomorphies (Watling et al. 1991; Pegler 2000). Besides, basidiomata are often not available to differentiate species, which further complicates the taxonomy of Armillaria (Harrington and Wingfield 1995). In this regard, Armillaria provides a clear example of where a phylogenetic approach can contribute significantly to its taxonomy. Until the late 1970s, Armillaria mellea was considered by most researchers to be a polymorphic species with a wide host range and distribution. Herink (1973), among others, suspected that this single species might be a species complex. However, since the morphology of basidiomata is difficult to study because of overlapping and inconsistent traditionally used morphological characters, other avenues of research were pursued. Hintikka (1973) developed a technique that allowed the determination of mating types in Armillaria. Using a modification of this method, Korhonen (1978a) was able to distinguish five European biological species. The cumbersome nature of the mating-type method of species identification prompted a search for other techniques for identifying collections. They were able to separate all North American species (NABS) of Armillaria except for A. calvescens and A. gallica, which are apparently very closely related (Anderson and Stasovski1992). Ten species of Armillaria in North America have been confirmed from multiple studies utilizing a combination of morphological, biological and phylogenetic species concepts (Anderson and Ullrich 1979; Anderson and Stasovski 1992; Burdsall and Volk 1993; Kim et al. 2006; Ross-Davis et al. 2012). Before, A. mellea shows great variability in morphology and hosts. These species were first separated using interfertility tests using cultures of Armillaria haploid tester strains and morphology. Now, A. mellea is considered as an independent species, with two North American biological species (Bérubé and Dessureault 1989; Volk et al. 1996) (Fig. 1). Molecular-based identification and diversity Problems surrounding the identification of Armillaria have led to important advances in developing robust but rapid DNA techniques. Such techniques have initially included DNA-base composition (Jahnke et al. 1987) DNADNA hybridization (Miller et al. 1994), sequence analyses of Fungal Diversity (2020) 103:87–218 91 Fig. 1 Disease cycle of Armillaria mellea (redrawn from Agrios 2005) the IGS-1(Anderson and Stasovski 1992) and ITS (Coetzee et al. 2001a, b), RFLPs without PCR (Smith and Anderson 1989) and RFLPs of IGS-1 amplicons (Harrington and Wingfield 1995). Although several of these techniques might pose some problems (Pérez‐Sierra et al. 2000), by their relative simplicity they have gradually replaced traditional, morphological methods. The amount of DNA sequence data on Armillaria species has increased substantially since the first publication on the phylogeny of the genus in the northern hemisphere (Anderson and Stasovski 1992). As with many other fungal genera, the focus of such studies initially was set on species of Europe and North America (Chillali et al. 1998; Coetzee et al. 2000b). Later, substantial datasets for species in Africa, Australasia and southeast Asia have become available (Terashima et al. 1998; Coetzee et al Coetzee et al. 2000a, 2001a). At present, ITS, IGS-1 and tef1 sequences are available in GenBank for the best-known species of Armillaria. However, there are disjunctions in data sets and relatively little is known about species from Indo-Malaysia and South America. Armillaria fruiting bodies are produced seasonally and not every year; they are, therefore, often not available during fieldwork (Kile et al. 1991). Identification using the biological species concept with species identification based on sexual compatibility tests (Korhonen 1978a) has been examined for its utility by some mycologists, but its application was soon abandoned. This was because of complications due to the absence of known tester strains, lack of haploid strains, ambiguous mating interactions and degeneracy of cultures. For these reasons, DNA-based molecular techniques have finally been preferred in Armillaria taxonomy, either complementing other methods or on their own. The techniques utilized for the taxonomy of Armillaria species include comparisons of RFLPs (Harrington and Wingfield 1995), AFLPs (PérezSierra et al. 2004), and the use of sequences from the ITS, IGS-1 and tef1 gene in phylogenetic studies (Coetzee et al. 2000b, 2001a; Maphosa et al. 2006; Kim et al. 2006). Phylogenetic methods have made it possible to differentiate the lineages of the genus in southern Argentina (Pildain et al. 2009). Lineages I and II grouped with A. novae-zelandiae and A. luteobubalina, respectively, while Lineages III and IV represented unique taxa that were closely related to A. hinnulea, Armillaria 4th species from New Zealand (established by Coetzee et al. 2001a, b) and Armillaria Group III from Kenya (Mwenje et al. 2006). Modern approaches to identification of Armillaria species are mostly based on the analyses of DNA sequences. The present study reconstructs the phylogeny of Armillaria based on a combined ITS, IGS and tef1 sequence data (Fig. 2, Table 2). However, insufficient data are available for the LSU gene region in GenBank. Then, it is difficult to have comparative phylogenetic analyses but the single gene analysis of each gene was carried out to compare the topology of the tree and clade stability. 13 92 13 Fungal Diversity (2020) 103:87–218 Fungal Diversity (2020) 103:87–218 ◂ Fig. 2 Phylogenetic tree generated by maximum likelihood analy- sis of combined ITS-IGS-tef1 sequence data of Armillaria species. Related sequences were obtained from GenBank. One hundred and thirty-nine strains are included in the analyses, which comprise 4557 characters including gaps. The tree was rooted with Guyanagaster lucianii (G31.4) and Guyanagaster necrorhizus (MCA 3950). Single gene analyses were carried out to compare the topology of the tree and clade stability. Tree topology of the ML analysis was similar to the MP and BYPP. ML phylogenetic tree inference was performed using RAxML version 8.2.12 on the CIPRES web server, using a mixed-model analysis and the GTRCAT model of substitution. The four partitions were defined as ITS, IGS, tef1 exons and tef1 introns. The best scoring RAxML tree with a final likelihood value of − 25308.198187 is presented. The matrix had 1957 distinct alignment patterns, with 65.74% of undetermined characters or gaps. Estimated base frequencies of ITS were as follows: A =0.227071, C =0.203923, G =0.235701, T =0.333305; substitution rates AC =0.628852, AG=3.751709, AT =1.365607, CG =1.467905, CT =2.788595, GT = 1.000000. Estimated base frequencies of IGS were as follows: A =0.244624, C =0.196588, G =0.242370, T =0.316418; substitution rates AC =0.954911, AG=3.055115, AT =1.041498, CG =1.278095, CT = 3.421100, GT = 1.000000. Estimated base frequencies of tef1 93 exons were as follows: A =0.228587, C =0.301128, G =0.255865, T =0.214420; substitution rates AC =0.905728, AG=3.660986, AT =1.564184, CG =0.648739, CT = 28.048363, GT = 1.000000. Estimated base frequencies of tef1 introns were as follows: A =0.215042, C =0.222693, G =0.185633, T =0.376631; substitution rates AC =1.170263, AG=5.878084, AT =0.847943, CG =1.087990, CT = 5.095797, GT = 1.000000; gamma distribution shape parameter α =0.1000000000. The maximum parsimonious dataset consisted of 2908 constant, 1172 parsimony-informative and 477 parsimonyuninformative characters. The parsimony analysis: CI = 0.610, RI = 0.861, RC = 0.525, HI = 0.390 in the first tree. Bayesian posterior probability was performed using the Markov chain Monte Carlo (MCMC) method implemented in MrBayes 3.2.6 with a mixed-model partition identical to the ones defined in the ML analysis. The best-fit nucleotide substitution model was separately determined for each partition with jModeltest version 2.1.10 on CIPRES, using the Akaike Information Criterion. K80+I, K80+I, SYM+G and HKY+G were selected as best-fit models for ITS, IGS, tef1 exons and tef1 introns, respectively. At the end of the runs, the average deviation of split frequencies was 0.016675. MP and RAxML bootstrap support value ≥ 50% and BYPP ≥ 0.95 are shown, respectively, near the nodes. Holotype or ex-type strains are in bold Fig. 2 (continued) 13 94 Fungal Diversity (2020) 103:87–218 Table 2 DNA barcodes available for Armillaria Species Sources Country Armillaria affinis A. altimontana JMCR.126 POR100* A. aotearoa A. borealis NZFRI-M 5283* CMW31075 CMW31072 HKAS 76263, Gt571 BRNM 699842, MUAF 501 CMW3172 A1 A5 A618 ST3 Central America? – USA AY213579, AY213580 New Zealand NR_151846 Belarus – China – China KT822294 AF261356 – – JN944606, JF313117 – KU295542 – KM205252 – KM205251 – KT822426 – KM205305 KM205304 – Czech Republic EU257713 – EU251402 EU257708 Finland Finland Germany Switzerland USA – JN657467 JN657468 JN657469 AY213559 DQ338540 – – – JF895899 – JN657440 JN657441 JN657442 AY509163 ST17 USA TH DJA 91/PUL F2895 BRNM 706814, MUAF 516 M110 HKAS 86583, 01108/1 B3 B5 Cameroon AY213560, AY213561 KU170952 DQ435623 JN657494 JN657495 JN657496 JF313138, JF895835 JF895900 JF313130, JF895836 KU170942 KU289112 – Czech Republic EU257715 – EU251395 EU257709 Canada China AY213581 KT822290 – – JF313121 KT822417 AY509182 – Finland Italy JN657445 JN657446 – – JN657418 JN657419, KJ414318 Japan UK? Ukraine USA Czech Republic China AB510853 – JN657450 AY213583 EU257716 KT822263 – – – – – – JN657472 JN657473 KJ414321 AB510786 JF746917 JN657477 JF313115 EU251396 KT822416 AB510809 JF288720 JN657423 AY509184 EU257710 – Korea Austria France France MG543860 EU257720 – KT822340 – – DQ338547 – MG544785 EU251403 FJ875698 KT822438 – EU257712 – – Japan Australia Ethiopia AB559000 AF329917 AY882969 – AB558992 DQ338552 DQ435646 – – – – AY172032 Kenya La Reunion Malawi South Africa Tanzania Zimbabwe Canada China AY882973 AY882974 AY882976 AY882971 AY882978 AY882967 AY213568 – – DQ338556 – – – – – – AY882965 AY882963 AY882959 AF204821 AY882961 AF489481 AY509171 KM205313 A. calvescens A. cepistipes A. ectypa A. fumosa A. fuscipes A. gallica 13 94-39-04 SY1Ra C5C-S1 W113 BRNM 695717 HKAS 86586, 97033/1 KFRI1616 BRNM 704974 CMW15693 HKAS 86565, 70011/13 TFM27105, Je-2 CMW4957, 123 CBS 118122, CMW5844, WG1I CMW7184 CMW4953 CMW4871 CMW2717 CMW4949 CMW4874 M70 CMW31087 ITS LSU tef1 – DQ435622 – – – – JF313123 KM205260 IGS1 – AY509181 AY509164 Fungal Diversity (2020) 103:87–218 95 Table 2 (continued) Species A. gemina A. heimii A. hinnulea A. jezoensis A. limonea A. lutea A. luteobubalina A. mellea Sources Country ITS LSU tef1 IGS1 HKAS 86569, 93421/1 BRNM 706835, MUAF 575 E4 86-016/3 86-008/2 NA4 MEX55 CMW7202 HY2a Aga235 ST22, EL-1 China KT822277 – KT822414 – Czech Republic EU257718 – EU251390 EU636240 France Germany Iran Japan Mexico South Africa Ukraine USA USA – – – – – – – JF895911 JF895912 Korea Korea Korea Canada USA – – – FJ618757 – JN657479 KJ200952 KJ200954 AB510761 KC111014 – JN657482 JF895847 JF313126, JF895848 MG544774 MG544784 MG544777 FJ618670 JF313136 JN657425 KJ200946 KJ200948 AB510834 JX281799 AY190245 JN657428 – AY509172 Ame10 KA14-1647 Ame7 JB-38A ST8 JN657452 – – AB510881 JX281809 AY190247 JN657455 – AY213569, AY213570 MG543850 MG543859 MG543852 FJ664586 AY213555 C4 166 K59 CMW4980 CMW4990 HUA9116 CMW4680 90-4 (Alut) CMW4977 AFTOL-ID449 B176 HKAS 86590, 00020/6 D1 B1212, CMW4615, 94056/1 B1205, CMW4613, 86009/1 CBS122232, CMW11265, 426 FFPRI420861, WD2588, 89-07 HKAS 86598, PFD84-103 MEX74 CMW3975 B916, CMW4610, A-5 HY-3 Am115 B927 CMW31161 Congo – Kenya Australia New Zealand Japan New Zealand USA Australia USA England China AY333917 AY333913 AY333916 – AF329905 – AF329930 – AF329912 AY789081 AF163578 KT822251 – – – DQ338555 DQ338555 – DQ338560 – DQ338559 AY700194 – – – – – DQ435648 DQ435648 – DQ435655 – DQ435657 AY881023 – KT822354 – – – – AY509158, AY509159 AY330630 AY330634 AY330627 AF445077 – D89921 AF445073 AF243066 AF445069 – AF163602 – France Hungary JN657464 AF163581 – – JN657491 – JN657437 AF163605 Iran AF163583 – DQ435637 AF163606 Italy FJ875692 FJ875694 DQ435636 – Japan AB510852 – AB510796 AB510808 Kenya KT822248 – KT822348 – Mexico South Africa South Korea JX281807 AF310329 AF163592 – – – KC111011 – DQ435639 JX281797 AF310327 AF163612 Ukraine USA USA China JN657466 – AF163595 – – JF895920 FJ875695 – JN657493 JF895856 DQ435634 KM205267 JN657439 – AF163608 KM205320 13 96 Fungal Diversity (2020) 103:87–218 Table 2 (continued) Species A. mexicana A. montagnei (ex luteobublina) A. montagnei (ex luteobublina) A. montagnei (Lineage II) A. montagnei (Lineage II) A. nabsnona A. novae-zelandiae A. novae-zelandiae (Lineage I) A. ostoyae A. puiggarii A. sinapina A. singula 13 Sources Country ITS LSU tef1 IGS1 CMW8082 HUA93110 MEX87* CMW5446 Bhutan Japan Mexico Argentina AY554333 – KR061310 AF448422 – – – DQ338562 – – KR061314 DQ435650 AY554335 D89922 KR061306 AF445068 CMW8876 Chile AF448423 – DQ435658 AF445065 Arg309 Argentina FJ660939 FJ711625 – – Arg270* Argentina FJ711609 – – – ST16 HKAS 85523, Gt798 M90 USA China AY213574 KT822333 – – JF313124 KT822411 AY509178 – Canada AY213573 – JF313122 00-3-1 C21 Japan USA AB510899 AY213572 – – AB510766 JF313119 CMW6905 Juk14411 CMW4967 CMW5448 CMW4143 CMW3951 CMW4722 Arg49 USA Korea Australia Chile Indonesia Malaysia New Zealand Argentina – MG543857 AF329921 AF448417 AF448421 AF448419 AF329926 FJ660935 DQ338542 – – DQ338554 DQ338564 DQ338553 DQ338551 FJ711629 DQ435631 MG544782 DQ435651 DQ435653 DQ435654 – DQ435652 – AY509176, AY509177 AB510850 AY509174, AY509175 – – – – – – – – SP308014* BRNM706815 CMW31102 HKAS 86579, 96043/11 C2 88-01-19 D20 HpAg1 P1404 Ame5 3626 MCA 3111/PUL F2896/BRG 41295 V48.5 M50 Brazil Czech Republic China China EF639348 EU257717 – KT822310 – – – – – EU251400 KM205272 KT822428 – EU257711 KM205325 – France Japan Switzerland Ukraine USA Korea Australia Guyana JN657459 AB510859 JN657463 JN657462 AY213554 MG543851 FJ664607 KU170954 – – – – – – FJ618752 KU254228 JN657486 AB510784 JN657490 JN657489 JF313140 MG544776 FJ618665 KU289104 JN657432 AB510815 JN657436 JN657435 AY509157 – – – Canada Canada FJ618763 – FJ618676 JF313114 – AY509167 China China FJ664609 AY213563, AY213564 – KT822323 – – KM205277 KT822422 KM205330 – Japan USA USA Japan AB510873 – AY213565 – – JF895916 – – AB510774 JF895850 JF313132 – AB510827 – AY509168 D89926 CMW31112 HKAS 86566, 96015/39 96-7-1 P2-7 ST12 HUA9101* Fungal Diversity (2020) 103:87–218 97 Table 2 (continued) Species Sources Country ITS LSU tef1 IGS1 A. socialis A. solidipes T2 MS2-11 CMW31107 PSpa86.5 Arg12 Arg25 CMW31118 99122/13 CMW3165 CMW31119 HKAS 86604, CT1097.3 96-1-8 HKAS 86605, 901582 HAt1S5 ATMUS2 France USA Finland Argentina Argentina Argentina China China France Italy Italy DQ784801 – – FJ664612 FJ660948 FJ660946 – KT822339 – – KT822338 – JF895918 – FJ618750 FJ711618 FJ711621 – – DQ338546 – – – JF895852 KM205275 – – – KM205280 KT822441 DQ435642 KM205281 KT822440 – – KM205328 – – – KM205333 – – KM205334 – Japan Slovenia AB510867 KT822337 – – AB510804 KT822439 AB510823 – Ukraine USA HQ232292 AY213588 – – HQ285906 JF313113 CMW10581 CMW31123 Bhutan China AY554329 – – – FJ875699 KM205284 HQ232284 AY509189, AY509190 AY624365 KM205337 CMW31124 CMW31127 China China – – – – KM205285 KM205286 KM205337 KM205339 CMW31128 CMW31136 China China – – – – KM205287 KM205293 KM205340 KM205346 CMW31138 CMW31140 China China – – – – KM205294 KM205296 KM205347 KM205349 CMW31142 CMW31144 China China – – – – KM205297 KM205298 KM205350 KM205351 CMW31145 CMW31146 China China – – – – KM205299 KM205300 KM205352 KM205353 CMW31148 CMW31150 China China – – – – KM205301 KM205302 KM205354 KM205355 CMW31151 HKAS 86615 HKAS 86621 HKAS 86623 HKAS 86551 HKAS 86613 HKAS 86614 HKAS 86602 HKAS 86606 HKAS 86574 HKAS 86574 HKAS 86570 HKAS 86571 China China China China China China China China China China China China China – KT822315 KT822306 KT822318 KT822279 KT822319 KT822305 KT822308 KT822281 KT822324 KT822327 KT822320 KT822288 – – – – – – – – – – – – – KM205303 KT822384 KT822386 KT822363 KT822367 KT822388 KT822391 KT822378 KT822359 KT822361 KT822364 KT822402 KT822404 KM205356 – – – – – – – – – – – – A. sparrei A. umbrinobrunnea A. tabescens Bhutanese Group 2 Chinese Biological species C Chinese Biological species F Chinese Biological species H Chinese Biological species J Chinese Biological species L Chinese Biological species N Chinese Biological species O Chinese Lineage 1 Chinese Lineage 2 Chinese Lineage 3 Chinese Lineage 4 Chinese Lineage 5 Chinese Lineage 6 13 98 Fungal Diversity (2020) 103:87–218 Table 2 (continued) Species Sources Country ITS LSU tef1 IGS1 Chinese Lineage 7 HKAS 83303 HKAS 83361 94-2-1 2000-71-13 China China Japan Japan KU378047 KU378048 AB510888 AB510879 – – – – KT822437 KT822436 AB510768 AB510773 – – AB510840 AB510832 Japanese Nag. E Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold This phylogenetic tree is largely in accordance with earlier studies from Coetzee et al. (2018) and provides the most conclusive phylogeny of the genera to date. Genealogical concordance phylogenetic species recognition (GCPSR) using the concordance among several gene trees (Taylor et al. 2000; Dettman et al. 2003) to delineate species has become standard in fungal taxonomy. However, except for a few studies (Guo et al. 2016; Tsykun et al. 2013), this taxonomic method has not been widely implemented in Armillaria taxonomy. Sequences of the genomes of key species are already providing prospects to study the evolution and systematics of Armillaria. They are certain to lead to important breakthroughs regarding not only the taxonomy but the biology and ecology of these fungi in the future (Sipos et al. 2017). Recommended genetic marker (genus level)—ITS Recommended genetic markers (species level)—ITS, IGS1, tef1 Additional genetic markers (species level)—LSU, tub2 Accepted number of species—There are 278 epithets in Index Fungorum (2020) listed for this genus. However, sequence data are only available for 31 species including 16 groups of unnamed species (Table 2). References—Watling et al. (1991), Pegler (2000), Harrington and Wingfield (1995) (morphology); Coetzee et al. (2000a, b, 2001a, b), Maphosa et al. (2006), Mwenje et al. (2006), Kim et al. (2006), Coetzee et al. (2018) (molecular phylogeny). 77. Barriopsis A.J.L. Phillips, A. Alves & Crous, in Phillips et al., Persoonia 21: 39 (2008) Background Stevens (1926) originally described the type species of Barriopsis in Physlospora as Physlospora fusca and Petrak and Deighton (1952) transferred it to Phaeobotryosphaeria. The fungus that was considered by Stevens (1926), and Petrak and Deighton (1952) did not have apiculi on its ascospores and was not similar to Phaeobotryosphaeria which had small, hyaline apiculi on the ascospores. von Arx and Müller (1954) considered Phaeobotryosphaeria as 13 a synonym of Botryosphaeria. Based on morphological difference and molecular sequence data, Phillips et al. (2008) introduced Barriopsis. Species of Barriopsis are mostly saprobic and weak pathogens (Phillips et al. 2013). Classification—Ascomycota, Dothideomycetes, Incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Barriopsis stevensiana A.J.L. Phillips & Pennycook Distribution—Species appear to be confined to regions with tropical or subtropical climates including Australia, Cuba, Iran and Thailand (Phillips et al. 2008; Abdollahzadeh et al. 2009; Liu et al. 2012; Phillips et al. 2013; Doilom et al. 2014; Konta et al. 2016; Dissanayake et al. 2016; Hyde et al. 2018b; Burgess et al. 2019). Disease symptoms—Barriopsis species can be weak pathogens and their pathogenicities are uncertain (Phillips et al. 2008; Dissanayake et al. 2016). Barriopsis stevensiana and B. iraniana were isolated from infected branches, fruits and leaves with various disease symptoms, including dieback, canker, rot and necrosis, from Cupressus sempervirens, Mangifera indica, Citrus sp. and Olea sp. in northern and southern provinces of Iran (Abdollahzadeh et al. 2009). Species of this genus may be future emerging pathogens. Hosts—Archontophoenix alexandrae, Cassia sp., Citrus sp., Mangifera indica, Olea sp. Tectona grandis (Phillips et al. 2008, 2013; Abdollahzadeh et al. 2009; Liu et al. 2012; Doilom et al. 2014; Konta et al. 2016; Dissanayake et al. 2016; Hyde et al. 2018b, 2020b). Pathogen biology, disease cycle and epidemiology Barriopisis in this article is considered as an emerging pathogen. Further studies to identify the biology, disease cycle and epidemiology are needed. Morphological based identification and diversity The sexual morph is characterized by brown aseptate ascospores that are widest in the center and lack terminal apiculi (Phillips et al. 2008, 2013; Doilom et al. 2014; Dissanayake et al. 2016; (Fig. 3)). Barriopsis archontophoenicis forms the sexual morph in culture medium after long Fungal Diversity (2020) 103:87–218 99 Fig. 3 Barriopsis stevensiana MFLU 19–1560. a Ascomata on dead twigs of Cassia sp. b Ascomata cut through horizontally showing the white contents with dark spots. c, d Sections through ascomata. e, f Ascospores. g Germinated ascospore. Scale bars: c, d = 200 µm, e, f = 20 µm, g = 100 µm periods of incubation (up to 6 months, Konta et al. 2016). The asexual morph is lasiodiplodia-like with hyaline conidia that become dark-brown and septate with irregular longitudinal striations (Stevens 1926). Abdollahzadeh et al. (2009) observed the asexual morphs of B. fusca and B. iraniana and confirmed that the morphology is similar to the description given by Stevens (1926). In their study, they revealed that this genus can be distinguished from other genera of Botryosphaeriaceae by the presence of visible striations on conidia at an early stage of development. However, using morphology alone in identifying these species is not wise due to the overlapping of morphological characters within the genus. Therefore, the use of multi loci phylogeny along with morphology is recommended for this genus. Very little is known about the diversity and pathogenicity of this botryosphaeriaceous genus and future studies are needed to confirm its pathogenic nature. Molecular based identification and diversity Phillips et al. (2008) using SSU, ITS, LSU, tef1 and tub2 sequence data established Barriopsis which is sister to Phaeobotryon. Based on ITS and tef1 sequence data, Abdollahzadeh et al. (2009) introduced B. iraniana. Doilom et al. (2014) introduced B. tectonae based on ITS, tub2 and tef1 sequence data. In this study, it was mentioned that ITS and tub2 sequence data have lesser variation, while tef1 sequence data have considerable variation. Konta et al. (2016) added a new species, B. archontophoenicis with the use of ITS, LSU, SSU and tef1 sequence data. In this study, we construct the phylogenetic tree for the accepted species based on ITS and tef1 sequence data (Fig. 4). Recommended genetic marker (genus level)—ITS Recommended genetic marker (species level)—tef1 Accepted number of species—There are six species epithets in Index Fungorum (2020), however only five species have DNA sequence data (Table 3). References—Phillips et al. (2008), Abdollahzadeh et al. (2009) (morphology and phylogeny); Dissanayake et al. (2016) (accepted number of species, phylogeny); Doilom et al. (2014), Konta et al. (2016) (new species). 78. Cercospora Fresen. ex Fuckel, Hedwigia 2(15): 133 (1863) Background Cercospora includes pathogens, saprobes and endophytes. Species are widely distributed, occurring on numerous flowering and ornamental plants, ferns, other fungi (as parasites), gymnosperms, grasses and other monocotyledons such as lilies, magnoliids and palms, mostly causing leaf spots. The well-known asexual morph, which is hyphomycetous, are 13 100 Fungal Diversity (2020) 103:87–218 Fig. 4 Phylogram generated from maximum likelihood analysis based on combined ITS, and tef1 sequence data of Barriopsis species and closely related taxa. Fifteen strains are in the combined sequence analyses, which comprise 865 characters including gaps. Diplodia mutila (CBS 112553 and CBS 230.30) was used as the outgroup taxa. Tree topology of the ML analysis was similar to the one generated from BI. The best scoring RAxML tree with a final likelihood value of − 2372.487246 is presented. The matrix had 201 distinct alignment patterns, with 12.30% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.207721, C = 0.288041, G = 0.271092, T = 0.233145; substitution rates AC = 1.068561, AG = 2.489613, AT = 0.682766, CG = 1.417925, CT = 4.236517, GT = 1.000000; gamma distribution shape parameter α = 1.343820. RAxML bootstrap support value ≥ 50% and BYPP ≥ 0.95 are shown respectively, near the nodes. Ex-type strains are in bold Table 3 DNA barcodes available for Barriopsis Species Isolate MFLUCC 14-1164* Barriopsis archontophoenicis B.iraniana IRAN 1448C* IRAN1449C B.tectonae MFLUCC 12-0381* B. thailandica MFLUCC 14-1190* B. stevensiana CBS 174.26* ITS tef1 KX235306 KX235305 FJ919663 FJ919665 KJ556515 KY115675 NR119698 FJ919652 FJ919654 KJ556516 KY115676 – Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold 13 among the largest groups of plant pathogenic fungi causing leaf spots, leading to diseases on many economically important crops (Agrios 2005; To-Anun et al. 2011; Groenewald et al. 2013; Guatimosim et al 2016; Park et al. 2017). Comparatively only a few sexual morphs have been studied (Hyde et al. 2013). A photosensitizing toxic compound named ‘cercosporin’ is responsible for Cercospora species inhabiting such a wide host range (Daub et al. 2005; Thomas et al. 2020). Classification—Ascomycota, Dothideomycetes, Dothideomycetidae, Capnodiales, Mycosphaerellaceae Type species—Cercospora apii Fresen., Beitr. Mykol. 3: 91 (1863) Distribution—Worldwide Disease symptoms—Leaf blights and spots Fungal Diversity (2020) 103:87–218 This disease affects the leaves, petioles, stems and peduncles of the tree. Infection and lesion formation initially occur on older leaves before progressing to newer ones. Small, brown flecks develop with a reddish border, expanding to circular spots with an ashy-grey centre. Concentric rings may be observed as individual lesions expand. This tissue becomes thin and brittle, and often drops out, leaving a ragged hole. These lesions often resemble frogeyes, giving this disease its common name. Severely affected leaves wither and die from coalescing lesions (Shane and Teng 1992; Steddom et al. 2005). Species of Cercospora cause blights and spots on the leaves, petioles, stems and peduncles of trees. Often infection and lesion formation occurs on older leaves before progressing to newer ones. Common symptoms include small, brown lesions that develop with a reddish border, eventually expanding to larger circular or angular spots. Concentric rings may be observed as individual lesions expand. The tissue becomes thin and brittle, and often drops out, leaving a ragged hole. Severely affected leaves wither and die from coalescing lesions (Shane and Teng 1992; Steddom et al. 2005). Hosts—Wide host range including plant genera in Amaranthaceae, Apiaceae, Asteraceae, Arecaceae, Chenopodiaceae, Convolvulaceae, Cryptogammaceae, Cucurbitaceae, Cyatheaceae, Dennstaedtiaceae, Dioscoreaceae, Euphorbiaceae, Fabaceae, Gunneraceae, Hydrangeaceae, Lamiaceae, Lygodiaceae, Musaceae, Myrtaceae, Onagraceae, Plumbaginaceae, Poaceae, Pteridaceae, Scrophulariaceae, Solanaceae, Thelypteridaceae and Urticaceae (Farr and Rossman 2020). Cercospora apii causes leaf spot disease on celery and C. beticola on sugar beet (Braun et al. 2013; Guatimosim et al. 2016). The pathogen Cercospora cf. sigesbeckiae infects various plant families, including economically valuable crops such as soybean, causing ‘Cercospora leaf blight’, a disease characterized by leaf bronzing (Albu et al. 2016, 2017). Some other species identified as causative organisms of the leaf blight are C. kikuchii and C. cf. flagellaris (Soares et al. 2015; Rezende et al. 2020). The yield losses related to Cercospora disease have been reported from Canada, China, India and other regions in the USA and South America (Almeida et al. 2005; Cai et al. 2009; Hershman 2009; Wrather et al. 2010; Geisler 2013; Albu et al. 2017; Bandara et al. 2020). Cercospora is among the leading fungal pathogens that cause a severe threat to soybean, which is an important grain legume crop, by reducing seed production and quality (Arantes et al. 2020). Two notable pathogens on soybean are C. kikuchii (leaf blight and purple seed stain) and C. sojina (frogeye leaf spot) (Soares et al. 2015) Other notable reports include Cercospora leaf spots, which are the most common and destructive of the Hibiscus diseases, often resulting in complete crop loss (Park et al. 2017) and more than 200 fungal species in association with 101 various diseases of ‘kenaf’ (Hibiscus cannabinus) worldwide (Park et al. 2017). Key proteins and expression of genes that could inhibit the pathogen C. kikuchii in soybean (Arantes et al. 2020) have been investigated. However, based on previous reports, morphological characters, phylogeny and pathogenicity of Cercospora cf. nicotianae was identified as one of several cryptic species causing Cercospora leaf blight (Sautua et al. 2019, 2020). Thomas et al. (2020) proposed the expression of fungal cercosporin auto resistance genes and silencing of the cercosporin pathway as effective strategies to combat Cercospora diseases. Pathogen biology, disease cycle and epidemiology The taxa survive on undecomposed residues in soil, on weed hosts and seeds. Leaf spot disease is favoured by warm, wet weather. Severe outbreaks generally require a period of showery weather. Infection from germinating fungal spores occurs via penetration of leaf stomata by fungal hyphae. Spores spread in wind, rain, irrigation or via mechanical tools (Vereijssen 2004; Lin and Kelly 2018). Morphological based identification and diversity Cercospora has been widely applied to all kinds of dematiaceous hyphomycetous asexual morphs characterized by holoblastic conidiogenesis and some associated with “Mycosphaerella”-like sexual morphs (Hyde et al. 2013; Groenewald et al. 2013). Species resembling the genus type, C. penicillata, characterized by pigmented conidiophores, thickened and darkened conidiogenous loci and singly formed colourless conidia are identified as Cercospora sensu stricto (Ellis 1971, 1976). Chupp (1954) published a worldwide monograph of this group which listed 1,419 species. A vast number of studies related to Cercospora are based on morphology or confined to specific regions or hosts (Phengsintham et al. 2013a, b). Hence, more than 3000 species of Cercospora have been described (Pollack 1987), often as a result of taxa being considered as hostspecific at a genus or family level (Crous and Braun 2003; Groenewald et al. 2005). However, based on morphological features of the structure of conidiogenous loci and hila, absence or presence of pigmentation in conidiophores and conidia, Crous and Braun (2003) revised the generic circumscription of Cercospora, resulting in the reduction of the number of species to 659. A series of publications related to Cercospora and its allied genera in Mycosphaerellaceae, along with illustrations and descriptions of sexual morphs was published by Braun et al. (2013, 2014, 2015a, b, 2016). Molecular based identification and diversity Cercospora is monophyletic (Stewart et al. 1999; Hyde et al. 2013). Groenewald et al. (2013) provided a comprehensive phylogenetic analysis of 360 isolates which included ITS, 13 and protein-coding genes; translation elongation factor 1-alpha (tef1), actin (act), calmodulin (cal) and histone 3 (his). This provided a basis for the identification of Cercospora species, indicating most to be host-specific (Park et al. 2017). Bakhshi et al. (2018) subjected 170 Cercospora isolates to an eight-gene analysis (tef1, act, cal, his, tub2, rpb2, gapdh) which resulted in several new clades within the C. apii, C. armoraciae, C. beticola, C. cf. flagellaris and Cercospora sp. G. complexes. The combination of tef1, cal, tub2, rpb2 and gapdh provided high phylogenetic resolution for distinguishing Cercospora species with gapdh being the gene effective in distinguishing the species complexes (Bakhshi et al. 2018). The genomes for several species—Cercospora arachidicola, C. aff. canescens, C. cf. sigesbeckiae, C. kikuchii, C. sojina and C. zeae-maydis have been published, of which C. cf. sigesbeckiae and C. sojina are important soybean pathogens (Albu et al. 2017; Sautua et al. 2019). The mating-type genes of some asexual Cercospora species have been characterised (Groenewald et al. 2013), of which C. beticola, C. zeae-maydis and C. zeina are heterothallic, while only one mating type was discovered in populations of C. apii and C. apiicola (Groenewald et al. 2006, 2010). In soybean cultivation regions such as China, Latin America or the USA, C. sojina occurs as several pathotypes named as races, and their existence differs from soybean cultivar-to-cultivar (Athow et al. 1962; Yorinori and Henechin 1978; Mian et al. 2008; Gu et al. 2020). Apart from being differentiated physiologically, several molecular genetic tools such as AFLPs (Amplified Fragment Length Polymorphisms), SSR markers and SNP markers have been utilized to characterize their population diversity (Gu et al. 2020). The combination of DNA sequence data with ecology, morphological and cultural characteristics named as the Consolidated Species Concept (Quaedvlieg et al. 2014) is an effective method for delimiting Cercospora species (Groenewald et al. 2013; Bakhshi et al. 2015, 2018). Here we provide an updated phylogenetic tree of combined ITS, tef1, act, cal, his, tub2, rpb2 and gapdh (Fig. 5). Recommended genetic markers (genus level)—LSU, ITS Recommended genetic markers (species level)—ITS, tef1, act, cal, his, tub2, rpb2, gapdh Accepted number of species—There are over 3100 epithets listed in Index Fungorum (2020), however, only 93 have DNA sequence data (Table 4). References—Braun et al. (2013, 2014, 2015a, b, 2016) (morphology), Groenewald et al. (2013) (morphology, phylogeny), Albu et al. (2017) (morphology, phylogeny), Guatimosim et al. (2016) (morphology, phylogeny), Bakhshi et al. (2015, 2018) (morphology, phylogeny). 13 Fungal Diversity (2020) 103:87–218 Fig. 5 The most parsimonious tree generated by MP analysis of combined ITS, tef1, act, cal, his, tub2, rpb2 and gapdh sequence data of Cercospora species is presented. Related sequences were obtained from previous publications and GenBank. One hundred and fourteen strains are included in the analysis comprising 4222 characters including gaps, of which 2942 characters are constant, 514 characters are parsimony-uninformative and 766 are parsimony-informative. The parsimony analysis of the data matrix resulted in the maximum of 84 equally most parsimonious trees with a length of 3092 steps (CI = 0.557, RI=0.678, RC = 0.382, HI = 0.443) in the first tree. The tree was rooted with Septoria provencialis (CBS 118910). Tree topology of the MP analysis was similar to the ML and BYPP analyses. ML and MP bootstrap support values ≥70% and BYPP ≥0.95 (ML/ MP/ BYPP) are shown respectively near the nodes. Ex-type strains are in bold. 79. Clinoconidium Pat., Bulletin de la Société Mycologique de France 14: 156 (1898) Background Clinoconidium is an important genus that causes smut disease on plants in the family Lauraceae. This genus was established by Patouillard (1898) and typified with Clinoconidium farinosum. Taxonomically, Clinoconidium is placed in Cryptobasidiaceae (Exobasidiales, Exobasidiomycetes, Basidiomycota) and characterized by aseptate, colourless, and globose to ovoid basidiospores which are dispersed individually. The name Clinoconidium was considered illegitimate because of the designation of an illegitimate type species name; however, it was later validated by Saccardo (1902). Clinoconidium is a gall producing genus which was once named as Ustilago by Ito (1935, 1936) due to the presence of a powdery spore mass on the surface of the galls. This genus was also transferred to another gall producing genus Melanopsichium by Kakishima (1982). However, it was renamed as Clinoconidium as its sorus structure and spore features are quite different from those of Ustilago (Saccardo 1902). The spores of Ustilago species are formed from sporogenous hyphae, whereas this fungus produces spores from hymenial layers in the galls. Spore walls are comparatively thinner than those of Ustilago. The differentiation from Melanopsichium, a gall producing taxon on plants in Polygonaceae (Vánky 2013) includes variation in gall structures and sporulation. Melanopsichium produces spores in chambers formed inside of gall tissues, while this genus produces spores in peripheral lacunae on the surface of gall tissues. The morphological characters of these taxa showed its close similarity to Clinoconidium. Classification—Basidiomycota, Ustilaginomycotina, Exobasidiomycetes, Exobasidiomycetidae, Exobasidiales, Cryptobasidiaceae Type species—Clinoconidium farinosum Pat. ex Sacc. & P. Syd Distribution—Brazil, China, Costa Rica, India, Japan, Panama, Spain, Taiwan and Venezuela ◂ 102 Fungal Diversity (2020) 103:87–218 103 13 104 Fig. 5 (continued) 13 Fungal Diversity (2020) 103:87–218 Fungal Diversity (2020) 103:87–218 Disease symptoms—mainly observed as powdery pappus gall in fruits. Infection initiates on very young fruits, converted into round, wrinkled galls. The fruit galls are then covered with a powdery mass of spores during early days of infection, withering in the rainy season, leaving behind hard, earthy, brown galls. On Cinnamon, entire young fruits are molded with buff and spongy smut like taxa in the full bloom of disease. Interestingly this infection is restricted to fruits only (Fig. 6). Hosts—different plants of Lauraceae including, Apollonias barbujana, Cinnamomum burmannii, C. camphora, C. daphnoides, C. tamala, C. tenuifolium, Nectandra sp., Octea sp., Oreodaphne sp. and Phoebe neurophylla (Farr and Rossman 2020). Morphological based identification and diversity This is an important pathogenic genus; producing galls on shoot buds of host plants belonging to the family Lauraceae. Fruits of the host are completely or partially transformed into reddish-brown to dark brown, irregularly malformed, enlarged, globose to subglobose galls; larger than normal fruits. Hymenia formed in peripheral lacunae of the galls are pale yellow to whitish and covered by the host epidermis. Inner tissues of galls consist of hyphae and deformed plant cells. Hyphae are intercellular, hyaline, compact, septate, smooth-walled and lack clamp connections, while haustoria are intercellular, slightly lobed to irregular and observed in deformed host cells. Upon maturation, galls rupture, exposing orange to dark brown or creamish white spore masses which cover the entire infected young fruits. Sterile hyphae can be found intermingled between the basidia in some species and are indistinguishable from young basidia or absent in some species of Clinoconidium. Basidia are clavate, hyaline, depressed, difficult to observe and gastroid, densely aggregated in masses, formed in irregular fascicles from basally agglutinated hyphae and the wall is densely foveolate when mature. Basidiospores are ellipsoid, clavate, pyriform, fusoid, globose, subglobose to oval, aggregated in a creamish white to brown coloured masses on the surface of the galls, hyaline or wall pale brown to brown, rugose when mature; producing long branched hyphae with septa when germinated on culture media and proliferating sympodially. Molecular based identification and diversity There are seven epithets of Clinoconidium recorded on various plant hosts. Sequence data for Clinoconidium bullatum, C. cinnamomi, C. onumae and C. sawadae are available in GenBank, including sequence data for LSU and ITS. Clinoconidium farinosum and C. globosum lack sequence 105 data in GenBank. ITS and LSU are the most suitable loci for f (Fig. 7). Recommended genetic markers (genus level)—ITS, LSU Recommended genetic markers (species level)—ITS, LSU Accepted number of species—There are seven species epithets in Index Fungorum (2020), however, only four species have DNA molecular data (Table 5). References—Hendrichs et al. (2003), Jiang and Kirschner (2016), Kakishima et al. (2017a, b) (morphology, phylogeny) 80. Cylindrocladiella Boesew., Canadian Journal of Botany 60 (11): 2289 (1982) = Nectricladiella Crous & C.L. Schoch, Studies in Mycology 45: 54 (2000) Background Boeswinkel (1982) established Cylindrocladiella to accommodate five Cylindrocladium-like species producing small, cylindrical conidia. Even though the generic status of Cylindrocladiella was initially opposed by Crous and Wingfield (1993), later studies on morphological comparisons by Crous et al. (1994) and molecular data (Victor et al. 1998; Schoch et al. 2000) supported the establishment of Cylindrocladiella as a genus. This genus is commonly confused with the asexual morph of Calonectria but can be distinguished by clear morphological differences, such as aseptate stipe extensions, different branching patterns of the conidiophores and comparatively small, aseptate conidia. Although species are generally not regarded as important plant pathogens, correct identification is essential for disease control and biosecurity implications. Classification—Ascomycota, Sordariomycetes, Hypocreomycetidae, Hypocreales, Nectriaceae Type species—Cylindrocladiella parva (P.J. Anderson) Boesew. Distribution—as a soil-borne fungus, the species in Cylindrocladiella have a cosmopolitan distribution in various geographically and climatically distinct regions around the world (Farr and Rossman 2020). Disease symptoms—black-foot disease, damping-off, leaf spot, root rot and shoot die-back Many species belonging to Cylindrocladiella are opportunistic plant pathogens but they are not considered as primary pathogens. They can be isolated associated with disease symptoms such as leaf spot, damping off and shoot die-back (Scattolin and Montecchio 2007; Pham 2018). Chocolate brown lesions around the shoots spread primarily to be followed by wilting of the shoot tip, reddish 13 106 discolouration, dropping of leaves, and finally plant death (Brielmaier-Liebetanz et al. 2013). Characteristic symptoms of the black-foot disease include a reduction in root biomass and root hairs with sunken and necrotic root lesions (Agustí-Brisach and Armengol 2013). Symptoms of Cylindrocladiella root rot are black lesions on the tap and lateral roots, wilting and foliar necrosis, and the outer bark of the seedlings will crack and become loose (Sinclair and Lyon 2005). Hosts—Species are soil-borne, weak pathogens of forestry, agricultural and horticultural crops. There are 270 records of Cylindrocladiella associated with different plant species (Farr and Rossman 2020). Among them, different Vitis species and Eucalyptus species are common hosts associated with different species of Cylindrocladiella. Morphological based identification and diversity Cylindrocladiella can be distinguished from related species by penicillate and/or subverticillate symmetrically branched conidiophores which produce small, cylindrical, 1-septate conidia and aseptate stipe extensions (Lombard et al. 2012). The generic status of Cylindrocladiella was earlier strongly contested (Sharma and Mohanan 1991), however, based on morphological evaluation and comparisons by Crous and Wingfield (1993) and Crous et al. (2017) confirmed its generic status. Victor et al. (1998) and Schoch et al. (2000) provided molecular data to support generic status. Lombard et al. (2012) in his revision of Cylindrocladiella mentioned that only two species have been recognized with their respective Nectricladiella sexual morph. Rossman et al. (2013) proposed that the generic name Cylindrocladiella be used rather than Nectricladiella. Lombard et al. (2015) showed that Cylindrocladiella formed a monophyletic group in Nectriaceae (Wijayawardene et al. 2020). Molecular based identification and diversity Using RFLPs and AT-DNA data, Victor et al. (1998) recognised seven species in the genus. Schoch et al. (2000) added another species based on ITS and partial tub2. Van Coller et al. (2005) introduced the use of his3 sequence data for this group. A combined multilocus phylogeny of his, tef1, tub2 and ITS was used by Lombard et al. (2012) which resulted in 18 new Cylindrocladiella species and several unresolved species complexes. Lombard et al. (2017) introduced six new species based on a combined ITS, tef1 and tub2 dataset. Pham (2018) introduced five new species based on his, tef1, tub2 and ITS sequence data and Marin-Felix et al. (2019) introduced two new species based on ITS, tef1 and tub2 sequence data. Here we reconstruct the phylogenetic analyses of these species based on ITS, tef1 and tub2 sequence data (Fig. 8). 13 Fungal Diversity (2020) 103:87–218 Recommended genetic markers (genus level)—ITS, LSU Recommended genetic markers (species level)—his, tef1, tub2 Accepted number of species—There are 47 species epithets in Index Fungorum (2020). However, only 46 species have DNA sequence data (Table 6). References—Crous and Wingfield (1993), Lombard et al. (2012) (morphology); Victor et al. (1998), Schoch et al. (2000), Lombard et al. (2015) (morphology, phylogeny). 81. Dothidotthia Höhn., Berichte der Deutschen Botanischen Gesellschaft 36: 312 (1918) Background Dothidotthia was assigned to Botryosphaeriaceae, because of its coelomycetous asexual morph, and characteristic peridium, pseudoparaphyses and asci (Barr 1989). Ramaley (2005) reported that Thyrostroma is the asexual morph of Dothidotthia based on the production of hyphomycetes in culture. Phillips et al. (2008), introduced a new family Dothidotthiaceae to accommodate Dothidotthia and considered Thyrostroma as the asexual morph of Dothidotthia. However, the links between the sexual and asexual morphs are not supported by molecular evidence. Recent molecular and morphology studies (Marin-Felix et al. 2017; Crous et al. 2019; Senwanna et al. 2019), based on a taxon sampling of current species indicates that Dothidotthia does not cluster near Thyrostroma. Thus, Dothidotthia is a distinct genus. Classification—Ascomycota, Pezizomycotina, Dothideomycetes, Pleosporomycetidae, Pleosporales, Dothidotthiaceae Type species—Dothidotthia symphoricarpi (Rehm) Höhn. Distribution—in both temperate and tropical countries (Italy, Russia, Thailand, Ukraine and the USA) Disease symptoms—species cause canker, dieback and leaf spot diseases on twig, branch, bark and leaf Hosts—Pathogens of Acer negundo, Diapensia lapponica, Fendlera rupicola, Euonymus alatus, Robinia pseudoacacia, Verbena asparagoides (Barr 1989; Farr and Rossman 2020; Index Fungorum 2020). Morphological based identification and diversity In previous studies, the asexual morphs of Dothidotthia have been reported as Thyrostroma (Ramaley 2005), however, phylogenetic analyses indicated that Dothidotthia can be separated from Thyrostroma (Marin-Felix et al. 2017; Crous et al. 2016; Senwanna et al. 2019). Dothidotthia is characterized by fusiform to obclavate or obpyriform, 0–3-transversely septate conidia and a sexual morph with clavate, short pedicellate asci, ellipsoid, 1-septate ascospores (Fig. 9). The sexual morphs of Dothidotthia and Thyrostroma have similar morphological characteristics in shape and overlapping Fungal Diversity (2020) 103:87–218 107 Table 4 DNA barcodes available for Cercospora Species Isolate no ITS tef1 act cal his tub2 rpb2 gapdh Cercospora achyranthis CBS 132613 JX143523 JX143277 JX143031 JX142785 JX142539 – – – CPC 10091 JX143524 JX143278 JX143032 JX142786 JX142540 – – – CBS 117292* AY647237 AY966897 AY966898 AY966899 AY966900 – – – C. agavicola# C. alchemillicola# CPC 5259* JX143525 JX143279 JX143033 JX142787 JX142541 – – – C. althaeina CBS 248.67* JX143530 JX143284 JX143038 JX142792 JX142546 MH496340 – MH496170 C. apii# CBS 116455* AY840519 AY840486 AY840450 AY840417 AY840384 MH496343 – MH496173 C. apiicola# CBS 116457* AY840536 AY840503 AY840467 AY840434 AY840401 – – – C. arecacearum P 521 KC677879 - - - - - - - C. ariminensis CBS 137.56 KF251297 KF253245 KF253606 KF253960 - KF252779 KF252303 - C. armoraciae# CBS 250.67* JX143545 JX143299 JX143053 JX142807 JX142561 MH496351 – MH496181 C. artemisiae LIPIMC 0769 KC776169 – – – – – – – C. asparagi# ICMP 21630 KY549097 KY549101 KY549091 KY549093 – – – – C. aurantia LSVM12 65 MG956773 – – – – – – – C. balsaminiana P608 KC677880 – – – – – – – C. beticola# CBS 116456* AY840527 AY840494 AY840458 AY840425 AY840392 MH496355 KT216555 MH496185 C. bidentis COAD 1018 JX117826 – – – – – – – C. bizzozeriana# CBS 258.67* JX143546 JX143300 JX143054 JX142808 JX142562 MH496368 – MH496198 C. brachiata COAD 2593 – MK118086 MK118087 – – – – – C. brassicicola Cer 68-18 MN209932 – – – – – – – C. broussonetiae P610 KC677882 – – – – – – – C. cf. brunkii CBS 132657 JX143559 JX143313 JX143067 JX142821 JX142575 – – – C. campi-silii CBS 132625 JX143561 JX143315 JX143069 JX142823 JX142577 – – – C. canescens# CPC 15871 JX143567 JX143321 JX143075 JX142829 JX142583 – – – CBS 111133 AY260065 DQ835084 DQ835103 DQ835130 DQ835157 – – – C. capsici# CBS 132622 JX143568 JX143323 JX143077 JX142831 JX142585 – – – C. capsicigena P289 KC677884 – – – – – – – C. caricis CG672 AF284390 – – – – – – – C. carotae CD1-1 KF941306 – – – KF941303 – – – C. celosiae CBS 132600 JX143570 JX143326 JX143080 JX142834 – – – – C. chenopodii# CBS 132594* JX143572 JX143328 JX143082 JX142836 JX142590 – – – CCTU 1060 KJ886438 KJ886277 KJ885955 KJ885794 KJ886116 MH496371 MH511862 MH496201 C. chinensis CBS 132612 JX143578 JX143334 JX143088 JX142842 JX142596 – – – C. christellae CCR22 isolate A FJ460222 – – – – – – – C. chrysanthemi LIPIMC 0759 KC776154 – – – – – – – C. chrysanthemoides CPC 20529 KC005779 KC005813 KC005764 KC005767 – – – – C. citrullina# CBS 119395 EU514222 JX143335 JX143089 JX142843 – – – – MUCC 576 JX143579 JX143337 JX143091 JX142845 – – – – C. cocciniae IPBCC 13.1008 KC776158 – – – – – – – C. codiaei LIPIMC 0779 KC776170 – – – – – – – C. coniogrammes CBS 132634* JX143583 JX143341 JX143095 JX142849 JX142603 – –– – C. convolvulicola CCTU 1083* KJ886441 KJ886280 KJ885958 KJ885797 KJ886119 MH496374 MH511865 MH496204 C. conyzae-canadensis CCTU 1119* KJ886445 KJ886284 KJ885962 KJ885801 KJ886123 MH496377 MH511868 MH496207 C. corchori MUCC 585* JX143584 JX143342 JX143096 JX142850 JX142604 – – – C. cf. coreopsidis CBS 132598 JX143585 JX143343 JX143097 JX142851 JX142605 – – – C. cryptomeriicola TFM:FPH7833 AB277789 – – – – – – – C. cylindracea CCTU 1081* KJ886449 KJ886288 KJ885966 KJ885805 KJ886127 MH496381 MH511872 MH496211 C. delaireae CBS 13259* JX143587 JX143345 JX143099 JX142853 JX142607 – – – C. dianellicola CBS 143453* MG386075 – MG674152 MG674153 – – – – C. dispori CBS 13260* JX143591 JX143349 JX143103 JX142857 JX142611 – – – C. cf. erysimi CBS 115059 JX143592 JX143350 JX143350 JX142858 JX142612 – – – C. euphorbiaesieboldianae CBS 113306* JX143593 JX143351 JX143105 JX142859 JX142613 – – – C. fagopyri CBS 132623* JX143594 JX143352 JX143106 JX142860 JX142614 – – – 13 108 Fungal Diversity (2020) 103:87–218 Table 4 (continued) Species Isolate no ITS tef1 act cal his tub2 rpb2 gapdh C. cf. flagellaris# CCTU 1159 KJ886493 KJ886332 KJ886010 KJ885849 KJ886171 MH496388 MH511879 MH496218 CBS 132653 JX143603 JX143361 JX143115 JX142869 JX142623 MH496390 MH511881 MH496220 CCTU 1204 KJ886505 KJ886344 KJ886022 KJ885861 KJ886183 MH496399 MH511890 MH496229 CBS 132667 JX143604 JX143362 JX143116 JX142870 JX142624 MH496401 MH511892 MH496231 CCTU 1172 KJ886501 KJ886340 KJ886018 KJ885857 KJ886179 MH496409 MH511900 MH496239 MH496240 CCTU 1154 KJ886489 KJ886328 KJ886006 KJ885845 KJ886167 MH496410 MH511901 C. gamsiana CCTU 1074* KJ886426 KJ886265 KJ885943 KJ885782 KJ886104 MH496446 MH511937 MH496276 C. cf. gossypii CCTU 1070 KJ886467 KJ886306 KJ885984 KJ885823 KJ886145 MH496452 MH511943 MH496282 C. helianthicola# MUCC 716 JX143615 JX143374 JX143128 JX142882 JX142636 – – – C. ipomoeae# CBS 132639 JX143616 JX143375 JX143129 JX142883 JX142637 – – – C. iranica CCTU 1137* KJ886513 KJ886352 KJ886030 KJ885869 KJ886191 MH496455 MH511946 MH496285 C. kikuchii CBS 128.27* DQ835070 DQ835088 DQ835107 DQ835134 DQ835161 – – – C. lactucae-sativae CBS 132604 JX143621 JX143380 JX143134 JX142888 JX142642 – – – C. malayensis KUS-F27687 KR400012 KY082663 KY082664 KY082665 KY082666 – – – C. cf. malloti MUCC 575 JX143625 JX143384 JX143138 JX142892 JX142646 – – – C. mercurialis CBS 550.71* JX143628 JX143628 JX143141 JX142895 JX142649 – – – C. cf. modiolae CPC 5115 JX143630 JX143389 JX143143 JXJX142897 JX142651 – – – C. cf. nicotianae CBS 131.32 DQ835073 DQ835099 DQ835119 DQ835146 DQ835173 – – – CBS 132632 JX143631 JX143390 JX143144 JX142898 JX142652 – – – C. olivascens CBS 253.67* JX143632 JX143391 JX143145 JX142899 JX142653 – – – C. cf.physalidicola SN150520 – KT275242 KT223391 KT275241 KT275240 – – – C. cf. physalidis# CBS 765.79 JX143633 JX143392 JX143146 JX142900 – – – – C. pileicola CBS 132607* JX143634 JX143393 JX143147 JX142901 JX142655 – – – C. plantaginis CBS 252.67* DQ233318 DQ233342 DQ233368 DQ233394 DQ233420 MH496461 – MH496291 C. polygonacea CBS 132614 JX143637 JX143396 JX143150 JX142904 JX142658 – – – C. pseudochenopodii CBS 136022* KJ886516 KJ886355 KJ886033 KJ885872 KJ886194 MH496464 MH511954 MH496294 C. punctiformis CBS 132626 JX143638 JX143397 JX143151 JX142905 JX142659 – – – C. cf. resedae CBS 118793 JX143639 JX143398 JX143152 JX142906 JX142660 – – – C. cf. richardiicola# CBS 132627 JX143640 JX143399 JX143153 JX142907 JX142661 MH496465 MH511955 MH496295 C. ricinella# CBS 132605 JX143646 JX143405 JX143159 JX142913 JX142667 – – – C. rodmanii CBS 113123 DQ835076 AF146136 DQ835122 DQ835149 DQ835176 – – – C. rumicis CCTU 1123 KJ886521 KJ886360 KJ886038 KJ885877 KJ886199 MH496466 MH511956 MH496296 C. rumicis CPC 5439 JX143648 JX143407 JX143161 JX142915 JX142669 – – – C. samambaiae CPC 24673 KT037514 KT037474 KT037596 KT037463 KT037555 – – – C. senecioniswalkeri CBS 132636 JX143649 JX143408 JX143162 JX142916 JX142670 – – – C. sesami Cers52-10 MK027103 – – – – – – – C. sidicola P500 KC677888 – – – – – – – C. cf. sigesbeckiae# CBS 132675 JX143655 JX143414 JX143168 JX142922 JX142676 – – – C. sojina CBS 132615 JX143659 JX143419 JX143173 JX142927 JX142681 – – – C. solani# CCTU 1043 KJ886523 KJ886362 KJ886040 KJ885879 KJ886201 MH496469 MH511959 MH496299 C. sorghicola CCTU 1173* KJ886525 KJ886364 KJ886042 KJ885881 KJ886203 MH496471 MH511961 MH496301 Cercospora sp. P CBS 116365* AY752141 AY752176 AY752204 AY752235 AY752266 – – – Cercospora sp. P JZG-2013 JX143714 JX143473 JX143227 JX142981 JX142735 – – – Cercospora sp. G CCTU 1197 KJ886540 KJ886379 KJ886057 KJ885896 KJ886218 MH496472 MH511962 MH496302 Cercospora sp. G CCTU 1015 KJ886528 KJ886367 KJ886045 KJ885884 KJ886206 MH496473 MH511963 MH496303 Cercospora sp. G CCTU 1090 KJ886536 KJ886375 KJ886053 KJ885892 KJ886214 MH496476 MH511965 MH496306 Cercospora sp. G CBS 115518 JX143681 JX143441 JX143195 JX142949 JX142703 MH496480 – MH496310 Cercospora sp. T CCTU 1148 KJ886541 KJ886380 KJ886058 KJ885897 KJ886219 MH496488 MH511976 MH496318 C. tagetea P609 KC677890 – – – – – – – C. tetragoniae HL_Tt-1 MT095118 – – – – – – – NFCCI3067* KC351743 KC513746 KC355808 KC513745 KC355807 – – – C. uwebaruniana CCTU 1200* KJ886408 KJ886247 KJ885925 KJ885764 KJ886086 MH496489 MH511977 MH496319 C. vignigena CBS 132611* JX143734 JX143493 JX143247 JX143001 JX142755 – – – 13 Fungal Diversity (2020) 103:87–218 109 Table 4 (continued) Species Isolate no ITS tef1 act cal his tub2 rpb2 gapdh C. violae# CBS 251.67* JX143737 JX143496 JX143250 JX143004 JX142758 MH496492 – MH496322 C. zeae-maydis# CBS 117757* DQ185074 DQ185086 DQ185098 DQ185110 DQ185122 – – – C. zebrina# CCTU 1225 KJ886550 KJ886389 KJ886067 KJ885906 KJ886228 MH496495 MH511981 MH496325 CCTU 1239 KJ886551 KJ886390 KJ886068 KJ885907 KJ886229 MH496504 MH511987 MH496334 C. zeina# CBS 118820* DQ185081 DQ185093 DQ185105 DQ185117 DQ185129 – – – C. cf. zinniae CBS 132624 JX143756 JX143518 JX143272 JX143026 – – – – CCTU 1003 KJ886552 KJ886391 KJ886069 KJ885908 KJ886230 MH496505 MH511988 MH496335 LIPIMC 0771 KC776162 – – – – – – – C. zinniicola Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with# Fig. 6 Clinoconidium sp. on Cinnamomum sp. a host plant with infected and healthy fruits, b healthy fruits, c, d infected fruits at various stages of infection dimensions of asci and ascospores (Barr 1989; Ramaley 2005; Phillips et al. 2008; Hyde et al. 2013; Senwanna et al. 2019). However, Dothidotthia can be differentiated from Thyrostroma by peridium structure and conidial morphology and molecular phylogeny (Senwanna et al. 2019). Crous et al. (2019) introduced Neodothidotthia to accommodate N. negundinicola and Dothidotthia aspera was synonymized under N. negundinis based on analysis of LSU sequence data. However, Senwanna et al. (2019) showed that Neodothidotthia negundinicola and N. negundinis group with D. robiniae and D. symphoricarpi (type species). Furthermore, the conidial morphology of Neodothidotthia is similar to Dothidotthia symphoricarpi (Pseudotthia symphoricarpi) and D. robiniae (Phillips et al. 2008; Zhang et al. 2012; Crous et al. 2019; Senwanna et al. 2019). Therefore, Neodothidotthia had been treated as a synonym of Dothidotthia. Molecular based identification and diversity Dothidotthia species can be separated from Thyrostroma based on LSU sequence data (Marin-Felix et al. 2017; Crous et al. 2019). Multigene phylogenetic analyses of a combined LSU, SSU, ITS and tef1 dataset for Dothidotthia is presented in this study, which is similar to Senwanna et al. (2019) (Fig. 10). Recommended genetic markers (genus level)—LSU, SSU Recommended genetic markers (species level)—ITS, tef1, rpb2 and tub2 Accepted number of species—There are 14 epithets listed in Index Fungorum (2020), however only four species have DNA molecular data (Table 7). References—Barr (1989), Ramaley (2005) (morphology); Phillips et al. (2008), Zhang et al. (2012), Hyde et al. (2013), 13 110 Fungal Diversity (2020) 103:87–218 Fig. 7 Phylogram generated from MP analysis based on combined sequences of LSU and ITS sequences of all the species of Clinoconidium with molecular data. Related sequences were obtained from GenBank. Five taxa are included in the analyses, which comprise 1100 characters including gaps, of which 910 characters are constant, 182 characters are parsimony-uninformative, eight characters parsimony-informative. The parsimony analysis of the data matrix resulted in the maximum of two equally most parsimonious trees with a length of 202 steps (CI = 0.980, RI 0.500, RC = 0.490, HI = 0.020) in the first tree Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted with Microbotryum violaceum (AFTOLID1819). Maximum parsimony bootstrap support value ≥ 50% and BYPP ≥ 0.9 are shown respectively near the nodes Table 5 DNA barcodes available for Clinoconidium obtain nutrients without killing host cells and without which they are unable to survive. As they are obligate plant pathogens, researchers have not had the advantage of routinely cultivating these taxa on artificial media. However, many powdery mildews have been grown on detached leaves of their hosts (Hirose et al. 2005). Powdery mildews seldom kill their host, but are responsible for water and nutrient loss and impaired growth and development. They can increase respiration and transpiration and interfere with photosynthesis and reduce yields. Changes in host range directly cause the niche separation of powdery mildews and thus may become a trigger of speciation in their evolution. It is possible that studying the evolutionary history of powdery mildews will not only reveal facts on fungal evolution but may also lead us to consider the evolutionary history of angiosperm plants (Takamatsu 2004; Matsuda and Takamatsu 2003; Hirata et al. 2000; Mori et al. 2000). The first systematic trial to identify the conidial states of powdery mildews at the species level was made by Ferraris (1910), who grouped species of Oidium according to the size and shape of their conidia and provided a key to its species. Foex (1913), Jaczewski (1927), and Brundza (1934) contributed to the classification of the conidiophore types. Jaczewski (1927) introduced the terms ‘Euoidium and Pseudoidium’ for Oidium states with catenate and solitary conidia, respectively. Yarwood (1957) provided a survey on the Erysiphaceae, including the asexual morphs. Species name Strain Name ITS LSU Clinoconidium bullatum C. cinnamomi C. onumae C. sawadae TUK-MA-01 – AB178259 R. Kirschner 4213 KX196602 KX196604 TUK-MA-02 – AB178260 R. Kirschner 4219 KX196600 KX196603 Marin-Felix et al. (2017), Crous et al. (2019), Senwanna et al. (2019) (morphology and phylogeny) 82. Erysiphaceae Tul. & C. Tul. [as ‘Erysiphei’], Select. fung. carpol. (Paris) 1: [191] (1861) Background Powdery mildews belong to Erysiphales of Ascomycota (Mori et al. 2000). Powdery mildews are one of the most prevalent and easily recognizable of plant diseases (Glawe 2008). Mucor erysiphe, published by Linnaeus (1753), was the first binomial referring to powdery mildew (now known as Phyllactinia guttata) (Braun and Cook 2012). Infections are often conspicuous owing to the profuse production of conidia that give them their common name. Powdery mildews are also models for basic research on host-parasite interactions, developmental morphology, cytology, and molecular biology (Glawe 2008). Erysiphaceae is obligately parasitic and as such, their life cycle depends completely on living hosts, from which they 13 Fungal Diversity (2020) 103:87–218 111 Fig. 8 Phylogram generated from MP analysis based on combined sequences of ITS, tef1 and tub2 sequences of all the accepted species of Cylindrocladiella. Related sequences were obtained from GenBank. Fourty-six taxa are included in the analyses, which comprise 2460 characters including gaps. Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted with Gliocladiopsis sagariensis (CBS 19955). The best scoring RAxML tree with a final likelihood value of − 6772.195394 is presented. The matrix had 261 distinct alignment patterns, with 0.96% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.230657, C = 0.279364, G = 0.252128, T = 0.237852; substitution rates AC = 1.388608, AG = 2.845402, AT = 2.389715, CG = 0.838197, CT = 7.220493, GT = 1.000000; gamma distribution shape parameter a = 0.650385. Maximum likelihood and MP bootstrap support value > 50% are shown respectively near the nodes. Ex-type strains are in bold Boesewinkel (1980) provided the first comprehensive key based on a combination of more than 12 morphological characteristics observed on conidia, conidiophores, appressoria, haustoria, fibrosin bodies, and mycelium. Braun (1987) issued a second comprehensive monograph of the Erysiphales encompassing all powdery mildew taxa known at that time. Shin and La (1993) and Shin and Zheng (1998) introduced some new morphological features of taxonomic 13 112 Table 6 DNA barcodes available for Cylindrocladiella Fungal Diversity (2020) 103:87–218 Species Isolate No ITS tef1 tub2 Cylindrocladiella addiensis C. arbusta# C. australiensis C. brevistipitata C. camelliae C. clavata C. cymbiformis C. elegans C. ellipsoidea C. hahajimaensis C. hawaiiensis C. horticola C. humicola C. infestans C. kurandica C. lageniformis C. lanceolata C. lateralis C. longiphialidica C. longistipitata C. malesiana# C. microcylindrica C. natalensis C. nederlandica C. novazelandica C. nauliensis C. obpyriformis# C. parva C. parvispora# C. peruvianum C. postalofficium C. pseudocamelliae C. pseudohawaiiensis C. pseudoinfestans C. pseudoparva C. queenslandica C. reginae C. solicola# C. stellenboschensis C. terrestris C. thailandica C. variabilis C. viticola# C. vitis# C. xishuangbannaensis CBS 143794* CMW 47295* CBS 129567* CBS 142786* IMI 346845 CBS 129564* CBS 129553* CBS 338.92* CBS 129573* MAFF 238172* CBS 129569* CBS 142784* CBS 142779* CBS 111795* CBS 129577* CBS 340.92* CBS 129566* CBS 142788* CBS 129557* CBS 116075* CMW 48278* CBS 111794* CBS 114943* CBS 152.91* CBS 486.77* CBS 143792* CMW 47194* CBS 114524 CMW 47197* IMUR 1843* CPC 37513* CBS 129555* CBS 210.94* CBS 114531* CBS129560* CBS 129574* CBS 142782* CMW47198* CBS 110668* CBS 142789* CBS 129571* CBS 129561* CBS 112897* CBS 142517* KUMCC 16-0146* MH111383 MH017015 JN100624 – AF220952 JN099095 JN099103 AY793444 JN099094 JN687561 JN100621 MF444911 MF444906 AF220955 JN100646 AF220959 JN099099 MF444914 JN100585 AF220958 MH017019 AY793452 JN100588 JN100603 AF220963 MH111387 MH017022 AF220964 MH017025 AF220966 MN562148 JN100577 JN099128 AF220957 JN100620 JN099098 MF444909 MH017021 JN100615 MF444915 JN100582 JN100643 AY793468 KY979751 MH388337 MH111393 MH016977 JN099060 MF444940 JN099087 JN098974 JN098988 JN099039 JN098973 JN687562 JN099057 MF444938 MF444933 JN099037 JN099083 JN099003 JN098978 MF444942 JN098966 JN098993 MH016981 JN099041 JN099016 JN099033 JN099050 MH111397 – JN099009 MH016987 JN098968 – JN098958 JN099012 JN099004 JN099056 JN098977 MF444936 MH016983 JN099051 MF444943 JN098963 JN099080 JN099064 KY979891 MH388372 MH111388 MH016958 JN098747 MF444926 AY793471 JN098752 JN098753 AY793474 JN098757 – JN098761 MF444924 MF444919 AF320190 JN098765 AY793481 JN098789 MF444928 JN098790 AY793506 MH016962 AY793483 JN098794 JN098800 AY793485 MH111392 MH016966 AY793486 MH016968 AY793500 MN556845 JN098814 JN098819 AY793508 JN098824 JN098826 MF444922 MH016964 JN098829 MF444929 JN098834 JN098719 AY793504 KY979918 – Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # relevance. A progressive report was provided by the work of Cook et al. (1997), who examined the surface of conidia by scanning electron microscopy and separated Oidium 13 into eight subgenera. Braun (1999) discussed the classification of Erysiphaceae as proposed by Cook et al. (1997) and introduced some corrections and alterations. Fundamental Fungal Diversity (2020) 103:87–218 113 Fig. 9 Dothidotthia robiniae (MFLU 16-1704). a, b Sporodochia on the host surface. c Vertical section of sporodochium. d Conidiogenesis. e, g Conidia attached with the conidiogenous cells. f, h Conidia. i Germinated conidium. Scale bars: b = 1000 µm, c = 200 µm, d–i = 30 µm innovations in the generic taxonomy of the group based on molecular and SEM examination and a better insight into the phylogeny are results of comprehensive investigations over the last decade (Takamatsu et al. 1998, 1999, 2000, 2005a, b, 2008; Matsuda and Takamatsu 2003; Hirose et al. 2005; Liberato et al. 2006; Braun and Cook 2012). Classification—Ascomycota, Pezizomycotina, Leotiomycetes, Leotiomycetidae, Erysiphales Type genus—Erysiphe R. Hedw. ex DC. Distribution—worldwide Disease symptoms—powdery mildew The initial signs of infection appear on young leaves in the form of small, raised blisters, which cause the leaves to curl and expose the under surfaces. As the disease progresses, round, pinpoint powdery white spots dusting the upper surfaces of leaves, as well as stems and occasionally fruiting occurs. As the disease becomes severe, the spots will become larger, and more interconnected and irregular in shape. Over time they progress from younger to older leaves and the undersides of leaves. However, mature leaves are usually much less severely infected than new or young leaves. If the white patches (which have a granular, powdery texture) are wiped away, the growths will return in a matter of days. Severely infected leaves will turn yellow, dry out and drop from the plant. Buds and growing tips of shoots can also become infected, eventually becoming distorted and stunted (Bushnell and Allen 1962; Davis et al. 2001; Romero et al. 2003; Oberti et al. 2014; Saharan et al. 2019). Hosts- The host range of this fungal group is strictly confined to angiosperms and powdery mildews have never been reported to infect ferns or gymnosperms (Amano 1986; Hirata et al. 2000; Takamatsu et al. 2010). They affect a wide range of angiosperms such as cereals and grasses, vegetables, ornamentals, weeds, shrubs, fruit trees, and broadleaved shade and forest trees. Powdery mildews are considered as host-specific. Pathogen biology, disease cycle and epidemiology Powdery mildews tend to grow superficially, or epiphytically, on plant surfaces. During the growing season, hyphae are produced on both the upper and lower leaf surfaces, although some species are restricted to one leaf surface. Infections can also occur on stems, flowers or fruit. Specialized absorption cells, termed haustoria, extend into the plant epidermal cells to obtain nutrition. While most powdery mildews produce epiphytic mycelium, a few genera produce hyphae that are within the leaf tissue; this is known as endophytic growth. Conidia are produced on plant surfaces during the growing season. They develop either singly or in chains on conidiophores. Conidiophores arise from the epiphytic hyphae, or in the case of endophytic hyphae, the conidiophores emerge through leaf stomata. At the end of the growing season, powdery mildews produce ascospores, 13 114 Fungal Diversity (2020) 103:87–218 Fig. 10 Phylogenetic tree generated by ML analysis of LSU, SSU, ITS and tef1 sequence data of Dothidotthia species. Related sequences were obtained from GenBank. The tree was rooted with Thyrostroma compactum (CBS 335.37) and T. lycii (MFLUCC 16-1170). Tree topology of the ML analysis was similar to the Bayesian analysis. The best scoring RAxML tree with a final likelihood value of − 5116.933762 is presented. The matrix had 115 distinct alignment patterns, with 25.41% of Table 7 DNA barcodes available for Dothidotthia Species undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.245094, C = 0.237101, G = 0.269739, T = 0.248067; substitution rates AC = 3.925871, AG = 7.445430, AT = 2.745308, CG = 2.728664, CT = 20.049514, GT = 1.000000; gamma distribution shape parameter α = 0.790240. Maximum likelihood bootstrap support values greater than 60% and BYPP probabilities ≥ 0.95 are indicated above the nodes. Ex-type (ex-epitype) and voucher strains are in bold Isolate no Dothidotthia negundinicola CBS 145039* MFLUCC 16-1157 MFLUCC 16-1183 D. negundinis CPC 12930 CPC 12932 CPC 12933 D. robiniae MFLUCC 16-1175* MFLUCC 16-1177 MFLUCC 16-1185 MFLUCC 18-0692 CPC 12929* D. symphoricarpi CBS 119687 LSU SSU ITS tef1 MK442537 MK751815 MK751816 EU673274 EU673275 EU673276 MK751817 MK751818 MK751819 MK751821 EU673273 MH874618 _ MK751760 MK751761 EU673226 EU673227 EU673228 MK751762 MK751763 MK751764 MK751766 EU673224 _ MK442597 MK751725 MK751726 MK442599 MK442600 MK442601 MK751727 MK751728 MK751729 MK751731 _ MH863064 _ MK908015 MK908016 _ _ _ MK908017 MK908018 MK908019 MK908021 _ _ Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold in a sac-like ascus enclosed in a fruiting body called a chasmothecium. The chasmothecium is generally spherical with no natural opening; asci with ascospores are released when a crack develops in the wall of the fruiting body. A variety of appendages may occur on the surface of the chasmothecia. 13 These appendages are thought to act as the hooks of a velcro fastener, attaching the fruiting bodies to the host, particularly to the bark of woody plants, where they overwinter. They can survive winter conditions as dormant mycelia within the buds and other plant tissue of the host. These infected parts Fungal Diversity (2020) 103:87–218 of the host can be the source of primary inoculum that can initiate further infection when conditions are right (Misra 2001; Amsalem et al. 2006; Heffer et al. 2006; Te Beest et al. 2008; Saharan et al. 2019; Fig. 11). Morphological based identification and diversity Members of Erysiphaceae cause powdery mildew disease on about 10,000 angiosperm species (Takamatsu et al. 2010). The Erysiphaceae are divided into five tribes and two basal genera (Cook et al. 1997). Both tree-parasitic and herb-parasitic species are included in three of the five tribes: Cystotheceae, Erysipheae and Phyllactinieae. Tree-parasitic species usually take basal positions in these tribes and herb-parasitic species have derived positions. The tribe, Golovinomycetea is a group derived from a single ancestor (Mori et al. 2000). The monophyly of the tribe is also supported by the common characteristics, i.e., ectophytic parasitism, polyascal ascomata, and Euoidium asexual morphs, with the latter producing conidia in chains without distinct fibrosin bodies. Of these five lineages, four consists of taxa infectious to dicotyledons. Blumeria graminis, which is infectious to monocotyledon plants, formed an independent lineage. Therefore, Blumeria graminis was accommodated in a monotypic tribe Blumerieae in the new system (Inuma et al. 2007). The powdery mildew belonging to the tribe Cystotheceae have both herbaceous and woody plants as hosts and consist of three genera, Cystotheca, Podosphaera and Sawadaea, of which Cystotheca and Sawadaea are restricted to a narrow range of host families (Meeboon et al. 2013). Podosphaera consists of two sections, Podosphaera and Sphaerotheca. Section Podosphaera parasitizes woody plants (Takamatsu et al. 2000). The tribe Golovinomyceteae consists of three genera, Golovinomyces, Neoerysiphe, and Arthrocladiella. Arthrocladiella is a monotypic genus consisting of a single species A. mougeottii and has only the host genus Lycium. Neoerysiphe is also a small genus composed of four species and has about 300 herbaceous host species ranging across five plant families including Lamiaceae. Golovinomyces is a large genus comprising 27 species (Braun 1987), and it is widely distributed in the world. The tribe Phyllactinieae comprises the genera Phyllactinia, Leveillula, Pleochaeta and Queirozia which typically have hemi-endophytic (partly external and partly internal mycelia in common (Braun 1987; Liberato 2007; Liberato et al. 2006; Khodaparast et al. 2001; Ramos et al. 2013). The tribe Erysipheae forms a separate, monophyletic clade, which is characterized by asexual morphs belonging to Oidium subgen. Pseudoidium Jacz (Takamatsu et al. 1999; Mori et al. 2000). This clade comprises Erysiphe and its sections Erysiphe, Microsphaera and Uncinula. Uncinula forestalis differs from the species of Erysiphe sect. Uncinula in having terminal, fasciculate, septate, ascoma appendages and Euoidium-like asexual morph (conidia catenate) and therefore it was placed in Caespitotheca (Takamatsu et al. 2005b). 115 Because of the lack of asexual morphs in Uncinula septata and U. curvispora and multiseptate chasmothecial appendages arising from the upper half the fruiting body, the two species were assigned to Parauncinula (Braun and Takamatsu 2000; Takamatsu et al. 2005a). A unique taxon, Oidium phyllanthi, on Phyllanthus acidus, P. amarus and P. reticulatus produces a germination type designated as Microidium-type and was placed in a new genus Microidium (To-anun et al. 2005). With these new classifications, Erysiphales contains 17 accepted genera, 16 based on the holomorph and one on the asexual morph (Braun and Cook 2012). With the descriptions of several new species, the number of recognized powdery mildew species has increased from 515 (including 435 sexual morphs/ holomorphs) in Braun (1987), to about 820 species (including about 685 sexual morphs/holomorphs) (Braun and Takamatsu 2000; Braun et al. 2002; Takamatsu et al. 2005a, b; Liberato et al. 2006; Braun and Cook 2012). Molecular based identification and diversity Molecular data have proven useful in reassessing species and clarifying the taxonomic significance of morphology and host data. Only a few of the described species have been reassessed using molecular data (Braun and Cook 2012). Reports began appearing in the 1990s, that used ITS and 18S rDNA sequences to infer phylogenetic relationships of Erysiphales and other major ascomycete groups (Saenz and Taylor 1999; Saenz et al. 1994). Analyses of 18S rDNA, ITS1–5.8S-ITS2, and 28S rDNA sequences led to the opinion that Erysiphales can be placed in Leotiomycetes along with Cyttariales, Helotiales, and Rhytismatales (Wang et al. 2006). Phylogenetic analyses demonstrated that Erysiphaceae formed a distinct monophyletic group (Hirata et al. 2000). Thus, Erysiphaceae is derived from a single ancestral taxon that may have acquired parasitism just once (Mori et al. 2000a; Takamatsu 2004; Wang et al. 2006). Shirouzu et al. (2020) using nrDNA and mcm7 sequence data showed that Phyllactinieae is not monophyletic. However, there is a need to re-assess the tribes in this family to establish them as subfamilies or genera. In this paper, we present a phylogenetic tree with combined ITS and LSU sequences obtained from available type material and voucher specimens (Table 8, Fig. 12). This can be used as a backbone in the identification of powdery mildew species. Recommended genetic markers (genus level)—ITS, LSU and SSU Recommended genetic markers (species level)—tub2, chs, tef1 The ITS region of the precursor molecules of rRNA was revealed to form a secondary structure including several stemloop structures, and some conserved sequences are found in the stem regions (Takamatsu et al. 1998). This makes it possible to design PCR primers that work for a wide range of the powdery mildews. Takamatsu and Kano (2001) designed 13 116 Fungal Diversity (2020) 103:87–218 Fig. 11 The life cycle of a powdery mildew fungus on roses. Redrawn from Agrios (2005) and Mulbrhan et al. (2016) four new PCR primers that are useful to determine the nucleotide sequences of the rDNA of the powdery mildews. These primers provide stability to work on a wide range of powdery mildews and specificity to eliminate contaminating DNA by PCR. Primer sets PM3/P3, ITS1/PM4, PM5/P3, and ITS1/ PM6 were tested with universal primer set ITS1/ITS4 (White et al. 1990) covering all major clades of Erysiphales. Meeboon and Takamatsu (2013a) used LSU, ITS and IGS (Inter generic spacer) sequences to identify two different genetic groups of Erysiphe japonica (= Typhulochaeta japonica), powdery mildew on Quercus species based on the differences in host range. Cho et al. (2014) used ITS and 28S rDNA for the introduction of the powdery mildew species Erysiphe magnoliicola in Erysiphe sect. Microsphaera. Wang et al. (2014) also used ITS differences for phylogenetic analysis of powdery mildew disease on mulberry in Yunnan Province. Meeboon and Takamatsu (2013b) also used the 28S rDNA sequences and a combined alignment of the 28S, ITS, and IGS (Intergeneric spacer) rDNA sequences to construct a phylogeny of Erysiphe sect. Uncinula on Carpinus species and showed the cryptic species Erysiphe paracarpinicola. de Oliveira et al. (2015) used ITS sequences of Erysiphe platani on Platanus × acerifolia in Brazil as new records of taxa. Liyanage et al. (2017) used ITS, SSU and LSU sequences to identify E. quercicola infected rubber trees. Phylogenetic analyses of B. graminis based on the DNA sequences of four DNA regions, i.e. ITS, 28S rDNA, chitin synthase 1, and ß-tubulin were conducted by Inuma et al. (2007) to revealed distinct groups in the B. graminis isolates from a single host genus belonged to a single group. 13 83. Fomitopsis P. Karst., Meddn Soc. Fauna Flora fenn. 6: 9 (1881) Background Fomitopsis was established by Karsten (1881) based on four species, with F. pinicola as the generic type (Murrill 1903; Donk 1960). The genus has a cosmopolitan distribution and comprises species causing brown rot on both living and dead trees (Han et al. 2016). Fomitopsis species also contribute to the decomposition of coarse woody debris in forest communities (Gilbertson 1980; Haight et al. 2019). There are certain instances of their pathogenic role in orchards of cultivated species where they cause heart rot on Citrus (Roccotelli et al. 2014) and Prunus species (Adaskaveg 1993). A Fomitopsis sp. was also recorded in oil palm (Elaeis guineensis) as an endophyte (Rungjindamai et al. 2008; Pinruan et al. 2010). Classification—Basidiomycota, Agaricomycetes, Incertae sedis, Polyporales, Fomitopsidaceae Type species—Fomitopsis pinicola (Sw.) P. Karst. Distribution—Worldwide Disease symptoms—Fomitopsis causes brown cubical rot on both living and dead trees (Mounce 1929). The basidiospores can be dispersed by wind, or by vectors such as bark beetles (Castello et al. 1976; Pettey and Shaw 1986; Lim et al. 2005; Persson et al. 2011; Jacobsen et al. 2017; Vogel et al. 2017). Upon infecting standing trees, stumps, or logs through wounds, or through the tunnels of penetrating vectors, the fungus establishes itself in the xylem (Mounce 1929). The growth rate of Fomitopsis species in the substrata Fungal Diversity (2020) 103:87–218 can differ depending on their ecological requirements (Markovic et al. 2011; Haight et al. 2019). When the decay starts, the wood turns yellowish-brown, which later splits into cubical fragments. The colour is generally lighter in case of F. pinicola than other agents of brown rot decay (Markovic et al. 2011). White mycelial felts can also develop in shrinkage cracks of the decayed wood (Ryvarden and Gilbertson 1993). After establishment, the perennial basidiome appears relatively rapidly (Mounce 1929, Fig. 13). The infection results in the breakage of treetops, or further infection of the base of the trees and weakening of larger roots, which may lead to eventual windthrow of standing trees. Hosts—The type species, F. pinicola mostly appears on gymnosperms, such as Abies, Larix, Picea and Pinus, but can also be found on angiosperms such as Acer, Alnus, Betula, Carpinus, Corylus, Elaeagnus, Fagus, Fraxinus, Malus, Populus, Prunus, Pyrus, Quercus, Salix, Sorbus, Tilia, Ulmus (Ryvarden and Gilbertson 1993; Dai 2012). The North American species in the Fomitopsis pinicola species complex have also been reported from Pseudotsuga, Sequioa and Tsuga (Haight et al. 2019). Other Fomitopsis species can be found on Ginkgo, Pinus and various angiosperm genera, such as Betula, Castanopsis, Cinamomum, Citrus, Delonix, Fagus, Eucalyptus Ligustrum, Prunus, Quercus and Tilia (Ryvarden and Gilbertson 1993; Dai 2012; Li et al. 2013; Han et al. 2016; Liu et al. 2019). Morphological based identification and diversity Based on morphological evidence, over 40 species were accepted in Fomitopsis (e.g. Ryvarden and Johansen 1980; Gilbertson and Ryvarden 1986; Ryvarden and Gilbertson 1993; Núñez and Ryvarden 2001; Hattori 2001). However, phylogenetic studies showed that the morphologically defined Fomitopsis was polyphyletic and taxa clustered with other brown-rot genera in the antrodia clade (Ortiz-Santana et al. 2013; Han et al. 2016). Han et al. (2016) showed that Pilatoporus and Piptoporus are synonyms of Fomitopsis sensu stricto, while the segregation of Rhodofomes was confirmed and five new genera were proposed. Fomitopsis sensu stricto is characterized by annual to perennial, mostly sessile, occasionally effused-reflexed or substipitate, soft, corky, tough to woody basidiocarps, a dimitic hyphal system with clamped generative hyphae and cylindrical to ellipsoid, hyaline, thin-walled, smooth basidiospores which are negative in Melzer’s reagent, and cause brown rot (Fig. 13). Molecular based identification and diversity Comprehensive multigene analyses by Han et al. (2016) accepted ten species in Fomitopsis sensu stricto. Two new Fomitopsis species were described from Brazil, F. flabellata and F. roseoalba (Tibpromma et al. 2017). Fomitopsis flabellata was transferred to Rhodofomitopsis and the new combination Fomitopsis bondartsevae was proposed (Soares et al. 117 2017). Mating studies and molecular phylogenetic analyses resolved four cryptic lineages in the F. pinicola species complex (Haight et al. 2016), that represents three North American species (F. mounceae, F. ochracea and F. schrenkii), and F. pinicola sensu stricto, which is restricted to Eurasia (Ryvarden and Stokland 2008; Haight et al. 2019). Three new species were proposed by Liu et al. (2019) from Australia (F. eucalypticola), Puerto Rico (F. caribensis), and China (F. ginkgonis). The phylogenetic tree of Fomitopsis presented here is based on analyses of a combined ITS, LSU, tef1 and rpb2 sequence data (Fig. 14). In our analyses, it appears that the type of F. bondartsevae is identical to F. iberica and F. hemitephra sensu stricto (Han et al. 2016), which are grouped close to F. palustris and other species formerly discussed in Pilatoporus. Therefore, a thorough revision of the pilatoporus clade is recommended to clarify the status of these species. Recommended genetic marker (genus level)—LSU Recommended genetic markers (species level)—ITS, tef1, rpb2 Accepted number of species—There are 104 epithets listed in Index Fungorum (2020). However, only 17 species have DNA sequence data (Table 9). References—Li et al. (2013) (phylogeny, new species), Han et al. (2016) (phylogeny), Haight et al. 2019 (phylogeny, new species), Floudas et al. (2012) (genome, F. pinicola), Hong et al. (2017) (genome, F. palustris), Liu et al. (2019) (phylogeny, new species). 84. Ganoderma P. Karst., Revue mycol., Toulouse 3(no. 9): 17 (1881) Background Ganoderma was established by Karsten (1881) based on G. lucidum and characterized by double-walled basidiospores with truncate apices and ornamented endospores, and a crusty or shiny pileus surface (Moncalvo and Ryvarden 1997). This genus was divided into two subgenera, Ganoderma and Elfvingia by Karsten (1889). Various authors used different taxonomic characters for the identification of species (e.g., Murrill 1902, 1903; Atkinson 1908; Coleman 1927; Corner 1947), which resulted in an intricate taxonomy, with 344 species names in speciesfungorum.org, but an estimated 180 species (He et al. 2019) and Steyaert (1972, 1980) worked extensively on the genus and introduced many new species, transferred many to the genus and removed several synonyms. Ryvarden (1985) and Gottlieb and Wright (1999a,b) studied the macro- and micromorphology. Ganoderma presently comprises sections Amauroderma and Ganoderma, subgenera: Ganoderma and Trachyderma (Index Fungorum 2020, Wijayawardene et al. 2020). Relevant characteristics for Ganoderma species delimitation are based on the macro and micromorphological characteristics (see in Fig. 15). The basidiomes are annual or 13 118 Fungal Diversity (2020) 103:87–218 Table 8 Genera in Erysiphaceae Genera Strain no Host ITS LSU Arthrocladiella Arthrocladiella mougeotii Blumeria Blumeria graminis Brasiliomyces Brasiliomyces malvastri SqGq-1 MUMH1723 NA JX546296 AB273556 NA AB022379 AB103065 NA Caespitotheca forestalis Cystotheca wrightii Cystotheca lanestris Erysiphe Erysiphe polygoni Erysiphe heraclei Erysiphe monascogera Erysiphe blasti Erysiphe juglandis Erysiphe hedwigii Erysiphe pulchra var. japonica Erysiphe symphoricarpi Erysiphe asiatica Erysiphe monoperidiata Erysiphe japonica var. crispulae Erysiphe adunca Erysiphe aphananthes Erysiphe flexuosa Erysiphe mori Erysiphe kenjiana Erysiphe prunastri var. prunastri Erysiphe wadae Golovinomyces Golovinomyces cichoracearum Golovinomyces adenophorae Golovinomyces cynoglossi Golovinomyces fischeri Golovinomyces leuceriae Golovinomyces Golovinomyces orontii Golovinomyces sonchicola Golovinomyces sordidus Golovinomyces sparsus Golovinomyces valerianae Leveilluta Leveilluta taurica Leveillula elaeagni Leveillula lactucae-serriolae Microidium Microidium phyllanthi Neoerysiphe Neoerysiphe cumminsiana Neoerysiphe galeopsidis Neoerysiphe galii Neoerysiphe geranii Neoerysiphe joerstadii Neoerysiphe kerribeeensis Neoerysiphe nevoi Parauncinula Parauncinula septata MUMH1461 KUS-F27309 NA UTC206 NA MUMH4190 MUMH2 MUMH48s VPRI 22225 MUMH90 MUMH1428 MUMH 4992 MUMH 4987 NA MUMH40 MUMH 4648 MUMH1429 NA KW:34760F MUMH776 MUMH1534 Lycium chinense Festuca arundinacea Malvastrum coromandelianum Schinopsis balansae Quercus glauca Quercus agrifolia Polygonum arenastrum Daucus carota Styrax japonica Lindera umbellata Microsphaera juglandis NA Cornus controversa Symphoricarpos albus Castanopsis diversifolia Castanopsis argyrophylla Quercus cuspidata NA Aphananthe aspera Aesculus hippocastanum Morus bombycis Ulmus minor Prunus domestica Fagus crenata AB193466 KF735066 AB000933 AF011307 AB000942 AB331647 AB015918 AB015928 AF298539 AB000941 AB078970 AB622218 AB622213 AB022416 D84383 AB69396 AB091774 AB000946 AB475118 AB046984 AB091776 AB193467 AB022355 AB022353 NA AB103371 NA NA NA NA AB022389 NA JQ220158 JQ220154 AB022415 AB022374 NA NA AB022418 AB475109 AB709961 NA MUMH623 MUMH144 MUMH3196 MUMH1343 MUMH1406 MUMH683 Mycelis muralis Adenophora triphylla var. japonica Cynoglossum asperrimum Senecio doronicum Leuceria thermarum AB077661 AB077633 AB769454 AB769450 AB246765 NA AB077632 AB077683 AB769452 NA MUMH2433 BCRU934 MUMH938 HMNWAFU-CF2011034 Cirsium japonicum Sonchus arvensis Plantago sp. Euphorbia collina Valeriana officinalis Triglochin maritime Elaeagnus angustifolia Hexinia polydichotoma AB769413 AB077673 AB769467 AB769461 AB769471 AY912077 AB048350 HQ821500 AB077678 AB077672 AB077657 NA NA NA NA HQ821501 Phyllanthus acidus Cacalia delphiniifolia Chelonopsis moschata Galium aparine Geranium sp. Phagnalon rupestre Senecio glossanthus Scolymus hispanicus Quercus cuspidata var. horikawae AB719943 AB329669 AB498949 AB498951 AB498956 AB498976 GU356546 AB498975 AB120758 NA AB022369 AB103365 AB498952 NA NA NA AB022420 Caespitotheca Cystotheca 13 Species name WSP71133 IRAN11138 NA MUMH(JPN)3361 MUMH 522 MUMH4680 MUMH 4682 MUMH4665 MUMH 4668 DAR 33493 MUMH 4671 MUMH585 AB183533 Fungal Diversity (2020) 103:87–218 119 Table 8 (continued) Genera Species name Strain no Host ITS LSU Phyllactinia Phyllactinia guttata Phyllactinia actinidiae Phyllactinia alni Phyllactinia betulae Phyllactinia- broussonetiaekaempferi Phyllactinia enkianthi Phyllactinia eupteleae Phyllactinia fraxini Phyllactinia guttata Phyllactinia juglandis Phyllactinia magnoliae Phyllactinia mali Phyllactinia moricola MUMH927 MUMH497 MUMH449 MUMH506 MUMH531 MUMH527 MUMH165 MUMH907 MUMH927 TUAMH2072 MUMH531 MUMH619 MUMHn36 AB080565 AB080508 AB080502 AB080507 AB080510 AB080504 AB080498 AB080543 AB080565 AB080531 AB080526 AB080523 AB080518 AB080456 HQ821501 AB080393 AB080398 AB080445 AB080408 AB080402 AB080453 AB080394 AB080422 AB080416 AB080414 AB080373 Pleochaeta Pleochaeta indica Pleochaeta shiraiana Podosphaera myrtillina Podosphaera leucotricha Podosphaera spiraeae Podosphaera cercidiphylli Podosphaera clandestine Podosphaera astericola Podosphaera balsaminae Podosphaera carpesiicola Podosphaera elsholtziae Podosphaera euphorbiaehirtae Podosphaera fusca Podosphaera fuliginea Podosphaera hibiscicola Podosphaera intermedia Podosphaera phtheirospermi Podosphaera pseudofusca Podosphaera xanthii Queirozia turbinata Sawadaea bicornis Sawadaea nankinensis Sawadaea polyfida Sawadaea tulasnei MUMH3208 MUMH20 NA HMLAC120001 MUMH 2490 MUMHS67 MUMH 2535 MUMH333 NA MUMH344 MUMHS131 MUMH319 NA MUMH809 MUMH605 MUMH331 MUMH774 MUMH346 MUMH74 Corylus sp. Actinidia arguta Alnus japonica Betula platyphylla var. japonica Broussonetia kazinoki Lyonia ovalifolia var. elliptica Euptelea polyandra Syringa vulgaris Corylus sp. Juglans mandshurica var. sachalinensis Magnolia quinquepeta Crataegus sp. Morus cathayana Celtis australis NA Vaccinium myrillus Photinia serrulata Spiraea cantoniensis Cercidiphyllum japonicum Spiraea japonica Aster ageratoides subsp. ovatus Impatiens balsamina Carpesium abrotanoides Ajuga reptans Acalypha australis NA Verbena spicata Hibiscus mutabilis Clerodendrum trichotomum Melampyrum nemorosum Fatoua villosa Youngia denticulata AB243757 D84380 NA JQ999954 AB525940 AB026140 AB525941 AB040335 FJ625796 AB040350 AB026142 AB040306 AF154324 AB046986 AB040308 AB026145 AB040332 AB040320 AB040351 NA VIC 26558 MUMH904 MUMH4232 MUMH486 MUMHS112 AB218773 AB193380 AB353762 AB193358 AB193388 NA AB022403 NA NA AB022384 NA AB103367 AB462779 AB462788 NA AB462794 AB462770 AB103369 AB462761 NA AB462777 NA NA JX512556 NA NA NA AB103370 NA AB193393 AB193400 Takamatsuella circinata NA NA NA Podosphaera Queirozia Sawadaea Takamatsuella Platycyamus regnellii Acer pseudoplatanus Acer buergerianum Acer amoenum var. matsumurae Acer mono var. marmoratum Stachys distans Type strains are in bold perennial, dimidiate, sessile or substipitate to stipitate, with distinctive non-laccate (dull) or weakly to strongly laccate, glossy, shiny, smooth, spathulate, furrows, which are sulcate on the pileus surface. Some strains have several layers of thick, dull cuticles or shiny, with thin cuticle or cuticle of clavate end cells. The context is cream to dark purplish brown, brown to dark brown, sometimes spongy to firmfibrous. Pores are 4–7 per mm, angular, entire, subcircular to circular, regular, mostly cream or white when young, light yellow to brown when mature, which are usually white to cream when fresh, turning pale yellow on drying, with bruising brown of pore surface. The tube layer is single or stratified, with pale to purplish brown, hard, and becomes woody when dry. The stipe is central or lateral when present. The Ganoderma hyphal system is di-trimitic and generative hyphae are thin-walled or occasionally thick-walled, with clamp connections. Skeletal hyphae are hyaline to brown, thick-walled, often long, unbranched. Binding hyphae are almost colourless, thin to thick-walled, branched and with clamp connections. Basidiospores are 7–30 μm 13 120 Fungal Diversity (2020) 103:87–218 Fig. 12 Phylogram generated from parsimony analysis based on combined ITS and LSU sequenced data Erysiphaceae. Maximum parsimony bootstrap support values greater than 60% and BYPP greater than 0.90 are indicated above the nodes. The type specimens (ex-epitypes) are in bold. The tree is rooted with Parauncinula septata long, usually broadly to narrowly ellipsoid, truncate, double-walled, and with an apical germ pore. The endosporium is brown and separated from the hyaline exosporium by inter-wall pillars, negative in Melzer’s reagent (Núñez and Ryvarden 2000; Ryvarden 2004). Basidia are broadly ellipsoid, tapering abruptly at the base, and cystidia are lacking. Ganoderma species are widely distributed in temperate, subtropical and tropical regions, and appear to thrive in hot and humid conditions (Pilotti et al. 2004; Hapuarachchi et al. 2019a, b; Luangharn et al. 2019). Basidiomes are commonly in the form of a bracket (Pilotti et al. 2004). Ganoderma is cosmopolitan and an important wood-decaying genus. Some 13 Fungal Diversity (2020) 103:87–218 121 Fig. 13 Fomitopsis pinicola a basidiomes on living European spruce, b causing brown-rot decay on narrow-leafed ash, c, d basidiomes on dead standing conifer tree, e young basidiome on hardwood log, f hyphal structure in the trama, g, h basidiospores. Scale bars: f = 20 µm, g, h = 5 µm species of Ganoderma are pathogenic, causing root and stem rot on a variety of monocotyledons, dicotyledons and gymnosperms, including a wide range of economically important trees and perennial crops which results in the death of affected trees (Hapuarachchi et al. 2018b). Ganoderma grows as facultative parasites of trees but can also live as saprobes on rotting stumps and roots (Turner 1981; Pilotti et al. 2004). Hence, they have ecological importance in the breakdown of woody plants for nutrient mobilization. Taxa also possess effective machinery of lignocellulose-decomposing enzymes which may be useful for bioenergy production and bioremediation (Hepting 1971; Kües et al. 2015; Hyde et al. 2019). Several Ganoderma species are prolific sources of highly active bioactive compounds such as polysaccharides, proteins, steroids and triterpenoids. These bioactive compounds show a huge structural and chemical diversity (Shim et al. 2004; Qiao et al. 2005; Wang and Liu 2008; Teng et al. 2011; De Silva et al. 2012a, b; 2013; Hapuarachchi et al. 2017; Li et al. 2018; Hyde et al. 2019). The bioactive constituents have anti-cancer, anti-inflammatory, anti-tumour, anti-oxidant, immunomodulatory, immunodeficiency, anti-diabetic, anti-viral, anti-bacterial, anti-fungal, anti-hypertensive, anti-atherosclerotic, anti-ageing, anti-androgenic, hepatoprotective and radical scavenging properties. They are also promising in neuroprotection, sleep promotion, cholesterol synthesis inhibition, preventing hypoglycemia, inhibition of lipid peroxidation/oxidative DNA damage, maintenance of gut health, prevention of obesity, and stimulation of probiotics (De Silva et al. 2012a; Hapuarachchi et al. 2016a, b, Hapuarachchi et al. 2017). Current studies are identifying secondary metabolites, developing models for prediction or early detection of diseases, finding biological control methods as well as understanding genomes. Using artificial neural network spectral analyses and foliage of four disease levels, Ahmadi et al. (2017) provided an early detection method for Ganoderma basal stem rot of oil palm. Sitompul and Nasution (2020) suggested that to control Ganoderma diseases non or weakly pathogenic fungi can be considered as biological control agents. These agents could break down woody debris faster than the pathogen and occupy the same resource as the pathogen (compete for nutrients) as well as producing inhibitory secondary metabolites (Paterson 2007; Sitompul and Nasution 2020). Utomo et al. (2018) sequenced the nuclear genome of G. boninense, the main pathogen of basal stem rot, and the draft genome comprised of 79.24 megabases and 26,226 predicted coding sequences. Ramzi et al. (2019) conducted a study to understand the plant cell wall degradation and pathogenesis of G. boninense via comparative genome analysis. In their study, they found that similarly to G. lucidium, G. boninense was enriched with carbohydrate-active and cell wall degrading enzymes. Following plant-host interaction analysis, several candidate genes including polygalacturonase, endo β-1, 3-xylanase, β-glucanase and laccase were identified as potential cell wall degrading enzymes that contribute to the plant host interaction and pathogenesis. The study provided fundamental knowledge on the fungal genetic ability and capacity to secrete carbohydrateactive and cell wall degrading enzymes. Agudelo-Valencia et al. (2020) pointed out that information regarding the biotechnological importance of Ganoderma species (other than G. lucidium) is quite limited. Therefore, in their study they obtained and studied the genome of G. australe, resulting in gene prediction for the 84-megabase genome, prediction of 22,756 protein-coding genes, prediction of five putative genes and two enzyme complexes from a ganoderic acid pathway. Most Ganoderma species are pathogenic or facultatively pathogenic, causing root and stem rot on a variety of monocotyledons, dicotyledons, and gymnosperms, including a wide range of economically important trees and perennial crops, which may result in death (Hapuarachchi et al. 2018a). Some species are saprobic and cause white-rot 13 122 Fungal Diversity (2020) 103:87–218 Fig. 14 Phylogram generated from RAxML analysis based on combined ITS, LSU, nSSU, tef1 and rpb2 sequence data of Fomitopsis species. Related sequences were obtained from GenBank. Thirty-one strains are included in the analyses, which comprised 4143 characters including gaps. The tree was rooted with Daedalea quercina (Dai 12152) and D. dickinsii (Yuan 1090). Tree topology of the ML analysis was similar to the Bayesian analysis. ML bootstrap values ˃ 50% and BYPP ˃ 0.80 are shown respectively near the nodes decay of wood (Muthelo 2009). Hence, they have ecological importance in the breakdown of woody plants for nutrient mobilization. They possess effective machinery of lignocellulose-decomposing enzymes useful for bioenergy production and bioremediation (Hepting 1971; Adaskaveg et al. 1991; Kües et al. 2015). Basal stem rot: Symptoms of basal stem rot disease can take several years to develop, and the presence of the pathogen is often only visible when the fungus is well-established and more than half of the tissue has been decayed. Soils with poor drainage and water stagnation during rainy seasons favour the disease (Kandan et al. 2010). Butt rot and root rot: The primary symptoms include wilting, mild to severe, of either all leaves or just the lowest leaves in the canopy, premature death of the oldest leaves or a general decline of the tree. The advanced decay of the larger roots is evident after leaves are blown down. Decay may extend from several cms to over a metre into the lower (butt) portion of the tree, depending on the species of Ganoderma. It is quite common for basidiomes not to appear before the severe decline and death of a tree (Glen et al. 2009). Therefore, the only way to determine if Ganoderma butt rot is the cause is to cut cross-sections through the lower Classification—Basidiomycota, Agaricomycotina, Agaricomycetes, Incertae sedis, Polyporales, Ganodermataceae Type species—Ganoderma lucidum (Curtis) P. Karst. 1881 Distribution—worldwide Disease symptoms—basal stem, butt and root rot in economically important trees and perennial crops, especially in tropical regions. Ganoderma disease development is affected by environmental factors and tree death could be either slow or rapid depending on water availability and temperature (Coetzee et al. 2015). 13 Fungal Diversity (2020) 103:87–218 Table 9 DNA barcodes for accepted species of Fomitopsis 123 Species Strain ITS LSU nSSU tef1 rpb2 Fomitopsis betulina F. betulina F. bondartsevae F. cana F. cana F. caribensis F. durescens F. durescens F. eucalypticola F. eucalypticola F. ginkgonis F. ginkgonis F. hemitephra F. iberica F. meliae F. meliae F. mounceae F. mounceae F. nivosa F. ochracea F. ochracea F. ostreiformis F. palustris F. pinicola F. pinicola F. roseoalba F. schrenkii F. schrenkii F. subtropica F. subtropica Dai 11449 Miettinen 12388 X1166* Dai 9611* Cui 6239 Cui 16871* Overholts 4215* O 10796 Cui 16598* Cui 16594 Cui 17170* Cui 17171 O 10808 O 10810 Ryvarden 16893 JV 1109/40-J JEH-78* MJL-112-Sp JV 0509/52-X JEH-12E JEH-79 Miettinen X1393 Cui 7615 Cui 10312 LT-323 URM 86923* JEH-150* JW18-240-1 Cui 10154* Cui 10578 KR605798 JX109856 JQ700276 JX435776 JX435777 MK852559 KF937293 KF937292 MK852562 MK852560 MK852563 MK852564 KR605770 KR605771 KR605776 KY264030 KF169629 KF169636 KR605779 KF169597 KF169604 KC595918 KR605780 KR605781 KF169651 KT189139 KU169365 KF169648 JQ067652 KR605787 KR605737 JX109856 JQ700276 JX435774 JX435775 MK860108 KF937295 KF937294 MK860113 MK860110 MK860114 MK860115 KR605709 KR605710 KR605715 – – – KR605718 – – KC595918 KR605719 KR605720 – KT189141 – – JX435772 KR605726 KR605895 – – KR605825 KR605826 MK860124 KR605835 KR605834 MK860129 MK860126 MK860130 MK860131 KR605841 KR605842 KR605849 – – – – – – – – KR605856 – – – – – KR605867 KR610726 JX109913 – KR610660 KR610661 MK900482 – KR610669 MK900484 MK900483 MK900485 MK900486 KR610675 KR610676 KR610681 – KF178354 KF178361 KR610686 KF178322 KF178329 – KR610688 KR610689 KF178376 – MK236356 KF178373 – KR610698 KR610816 JX109884 – KR610762 KR610761 MK900474 – KR610766 MK900479 MK900476 MK900480 MK900481 – KR610771 KR610775 – KF169698 KF169705 KR610777 KF169666 KF169673 – KR610779 KR610780 KF169720 – MK208858 KF169717 – KR610791 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold meter or so of the trunk after the tree is felled and examine the cross-sections for the typical pattern of rot: greatest near the soil line, decreasing in sections further from the soil line. Ganoderma root rot may cause yellowing, wilting, or undersized leaves and dead branches. Tree vigour may decline as the decay of the sapwood advances. The first visible sign of infection is often the formation of basidiomes (solitary or in clusters) on the lower trunk and exposed root areas. There are two types: varnished and unvarnished. The upper surface of varnished fungus rot is typically red-brown with a white edge, shiny, and lacquered. Conks of the unvarnished fungus rot are brown with a white edge weathering to grey (Pilotti et al. 2004). When fresh, both have a white, porous surface on the underside. The rate of decay can lead to death in as little as 3 to 5 years from the time of infection and appears to be determined by tree vigour, which is often influenced by environmental stresses (Nirwan et al. 2016). Hosts—Ganoderma has a wide host range, with more than 44 species from 34 potential host genera identified (Venkatarayan 1936). The root and stem rots caused by Ganoderma species, result in decreased forestry yields of e.g. Areca catechu (Palanna et al. 2020), Camellia sinensis, Cocos nucifera, (Kinge and Mih 2014), Elaeis guineensis, (Glen et al. 2009) and Hevea brasiliensis (Monkai et al. 2017) worldwide. Pathogen biology, disease cycle and epidemiology The fungus is spread by spores produced in the prominent basidiomes that form on the outside of the tree (conks). New spores released from the conks are dispersed throughout the summer during humid periods and infect open wounds on root flares and lower trunk areas of susceptible trees. The spores germinate, and the infection progresses to attack the sapwood of major roots and the lower tree trunk. Over the years, the number of decayed wood increases leading to 13 124 Fungal Diversity (2020) 103:87–218 Fig. 15 Morphology of Ganoderma species. a An old basidiome of Ganoderma australe, b Mature basidiome of G. casuarinicola, c, d hyphae, e tube layer hyphae, f–h Basidiospores, i Pore characteristics. Scale bars: a, b = 2 cm; c, d = 3 μm; e = 15 μm; f, g, h. = 5 μm; i = 500 μm 13 Fungal Diversity (2020) 103:87–218 dangerously soft, spongy wood in the part of the tree that functions as its anchor (Paterson 2007). Morphology-based identification and diversity Ganoderma species identification, limitations and their taxonomic segregation have been unclear and recently being debated (Moncalvo et al. 1995; Wang et al. 2009; Cao et al. 2012; Yao et al. 2013; Richter et al. 2015; Zhou et al. 2015a, b). Many Ganoderma collections and species have been misnamed because of the presence of heterogenic forms, taxonomic obstacles and inconsistencies in the way the genus has been subdivided (Mueller et al. 2007). Ganoderma species are genetically heterogeneous, hence a wide range of genetic variation has been reported and caused by outcrossing over generations and different geographical origins (Pilotti et al. 2004). This has led to variation in their listed morphological characteristics, even within the same species (Hong et al. 2001). Environmental factors, variability, inter hybridization and individual morphological bias, mean identification of Ganoderma species is difficult (Zheng et al. 2007a). Hence, naming a species is confused and traditional taxonomic methods based on morphology are inconclusive for establishing a stable classification system for Ganoderma species (Hseu et al. 1996; Hong et al. 2001) which in turn result in an uncertain nomenclature. This confusing situation is mainly the result of various criteria used in identification by different authors. Some authors strictly only focus on hostspecificity, geographical distribution and macro morphology of basidiomes, while other authors only focus on spore characteristics as the primarily taxonomic characteristics (Sun et al. 2006; Ekandjo and Chimwamurombe 2012). Richter et al. (2015) suggested using a combination of morphological, chemotaxonomic and molecular methods to develop a more stable taxonomy for this genus. Molecular identification and diversity Isoenzyme analysis was the first molecular technique used to separate Ganoderma species (Park et al. 1994; Gottlieb et al. 1995, 1998; Gottlieb and Wright 1999a, b; Smith and Sivasithamparam 2000). Then, DNA sequences of the internal transcribed spacer (ITS), partial large subunit rDNA (Moncalvo et al. 1995, 2000; Cao et al. 2012; Yao et al. 2013; Richter et al. 2015) and nearly complete small subunit rDNA sequences (Hong and Jung 2004; Douanla-Meli and Langer 2009) were used. Later, multigene phylogenetic analyses with protein-coding genes such as β-tubulin (tub2), the largest subunit of RNA polymerase II gene (rpb1), the secondlargest subunit of RNA polymerase II (rpb2), and translation elongation factor 1-α (tef1) were performed to resolve the taxonomic confusions within Ganoderma (Park et al. 2012; Zhou et al. 2015a, b; Hennicke et al. 2016; Jargalmaa et al. 2017). However, many problems remain in the resolution of 125 phylogenetic relationships within the genus. As a result of the intricate taxonomy of Ganoderma, 65% of the Ganoderma sequences available in GenBank were reported to be wrongly identified or ambiguously labelled, (Jargalmaa et al. 2017). In this study, we reconstruct the phylogenetic tree based on ITS, tef1 and rpb2 sequence data (Table 10, Fig. 16). Recommended genetic marker (genus level)—ITS Recommended genetic markers (species level)—rpb2, tef1 Accepted number of species—There are 456 species and infra-species epithets in Index Fungorum (2020), for 224 accepted species. However, only 64 species have DNA sequence data. References—Coetzee et al. (2015); Xing et al. (2016, 2018); Tchoumi et al. (2019), Luangharn et al. (2019), Ye et al. (2019) (phylogeny, new species), Cabarroi-Hernández et al. (2019) (phylogeny). 85. Golovinomyces (U. Braun) V.P. Heluta, Biol. Zh. Armenii 41: 357 (1988) Background Braun (1978) introduced Golovinomyces as a section of Erysiphe sensu lato and Heluta (1988a) raised it to genus rank. Braun (1999) and Braun and Takamatsu (2000) accepted Golovinomyces as a distinct genus and established a new tribe, Golovinomyceteae. This is a strictly herb-parasitic genus in the Erysiphaceae. Host-parasite co-speciation was reported between Golovinomyces and Asteraceae hosts using molecular phylogenetic analyses (Matsuda and Takamatsu 2003). It was suggested that Golovinomyces first acquired parasitism on Asteraceae and then diverged to the host tribes Astereae, Cardueae, Heliantheae and Lactuceae. Bremer (1994) pointed out that Golovinomyces may have originated in South America and the geographic distribution expanded into the Northern Hemisphere. However, Takamatsu et al. (2006) suggest that Golovinomyces originated in the Northern Hemisphere, and not in South America. Fabro et al. (2008) profiled genome-wide expression on haustorium formation of G. cichoracearum in Arabidopsis. Research to understand pathogenesis towards plants has been undertaken. A draft whole genome of G. magnicellulatus, the causal agent of phlox powdery mildew was provided by Farinas et al. (2019). McKernan et al. (2020) identified 82 genes associated with resistance to G. chicoracearum, the causal agent of powdery mildew in cannabis. Classification—Ascomycota, Pezizomycotina, Leotiomycetes, Leotiomycetidae, Erysiphales, Erysiphaceae Type species—Golovinomyces cichoracearum (DC.) V.P. Heluta Distribution—Worldwide (Mainly in northern hemisphere) Disease symptoms—powdery mildew 13 126 Hosts—Has a wide range of hosts including Asteraceae, Boraginaceae, Cucurbitaceae, Malvaceae, Fabaceae, Lamiaceae, Polygonaceae, Scrophulariaceae, Solanaceae and Verbenaceae. Pathogen biology, disease cycle and epidemiology Discussed under Erysiphaceae. Morphological based identification and diversity Golovinomyces is characterized by chasmothecia with mycelioid appendages, several, mostly 2-spored asci, an asexual morph with catenescent conidia that lack fibrosin bodies, and mostly nipple-shaped appressoria (Braun 1978; Qiu et al. 2020a). Heluta (1988a) reallocated Erysiphae cichoracearum to Golovinomyces and now nearly all species of E. cichoracearum are assigned to Golovinomyces. Braun (1987) confined E. cichoracearum to powdery mildews on hosts of Asteraceae and assigned specimens on hosts belonging to other plant families to Erysiphe orontii. Braun and Cook (2012) split G. cichoracearum into several species based on molecular analyses of this complex which suggested a co-evolutionary relationship between Golovinomyces species and tribes of Asteraceae (Matsuda and Takamatsu 2003). Golovinomyces cynoglossi sensu lato, a complex of morphologically similar powdery mildews on the plant family Boraginaceae, was reassessed by Braun et al. (2018) and split into G. asperifoliorum, G. asperifolii and G. cynoglossi based on sequence analyses, biological aspects and morphological differences. Braun et al. (2019) revisited G. orontii and Qiu et al. (2020b) epitypfied and confirmed Erysiphe cucurbitacearum was a synonym of G. tabaci. Molecular based identification and diversity A comprehensive phylogenetic analysis by Takamatsu et al. (2013) resulted in a polyphyletic complex that split into three genetically distinct clades. Golovinomyces ambrosiae and G. spadiceus were considered as separate species by Braun and Cook (2012). However, phylogenetic analyses of ITS and 28S rDNA sequences by Takamatsu et al. (2013), including Golovinomyces species on Asteraceae, found that these two species that occur on Asian species of Eupatorium and a multitude of other hosts, including those on other plant families, formed a single large, unresolved clade (lineage III in Takamatsu et al. (2013)). The taxonomic interpretation posed a serious problem as G. ambrosiae and G. spadiceus were treated as two morphologically differentiated species. Hence, the resolution based only on ITS sequence data was considered insufficient to distinguish closely allied species. Most subsequent authors followed the taxonomic treatments in Braun and Cook (2012) and recognized G. ambrosiae and G. spadiceus as separate species, within lineage III, based 13 Fungal Diversity (2020) 103:87–218 on morphological differences (Qiu et al. 2020a). However, there is minimal multi loci data for the powdery mildews currently available. Most of the research involves the intra-specific genetic diversity in species such as Blumeria graminis (Walker et al. 2011), Erysiphe necator (de Oliveira et al. 2015), Golovinomyces orontii (Pirondi et al. 2015a) and Podosphaera xanthii (Pirondi et al. 2015b). Based on ITS and D1/D2 domain of 28S sequence data, Braun et al. (2019) introduced G. bolayi and G. vincae. Nayak and Bandamaravuri (2019) developed species-specific PCR primers CgF2 and CgR2 for G. orontii (the causal agent of powdery mildew in cucurbits), based on partial ITS and 5.8S rDNA, which resulted in a 233bp fragment of G. orontii. Recommended genetic markers (genus level)—ITS, LSU Recommended genetic markers (species level)—Comprehensive applications of multi loci approaches to solve complex taxonomic-phylogenetic problems connected with the species level classification of the powdery mildews are lacking. The phylogenetic analyses of multi loci sequence data, including ITS and LSU, IGS, tub2, chs, and consideration of morphological characters resolve species delimitation in a heterogeneous complex within Golovinomyces. Accepted number of species—There are 81 epithets listed in Index Fungorum (2020), however, only 41 have molecular data (Table 11, Fig. 17). References—Braun (1978, 1987), Heluta (1988a, b) (morphology); Braun and Cook (2012), Takamatsu et al. (2013), Braun et al. (2019), Qiu et al. (2020a, b) (morphology and phylogeny). 86. Heterobasidion Bref., Unters. Gesammtgeb.Mykol. (Liepzig) 8: 154 (1888) Background Heterobasidion was introduced by Brefeld (1888) and is typified by H. annosum (≡ Polyporus annosus). Certain Heterobasidion species are important forest pathogens of the Northern Hemisphere, causing root and butt rot, mainly in conifers (Woodward et al. 1998). In coniferous plantations, Heterobasidion is one of the most widespread of wood decay agents, especially when the host is under intensive management. Heterobasidion greatly reduces site productivity and the amount of harvestable timber; estimated financial losses caused by Heterobasidion species in Europe were around 800 million euro per year (Korhonen et al. 1998; Garbelotto 2004; Asiegbu et al. 2005). On the other hand, these taxa have a relatively moderate pathogenic role in natural forest ecosystems. They affect stand species composition, density and structure, and they contribute to forest succession, nutrient recycling and even regeneration (Goheen and Otrosina 1998; Garbelotto 2004; Dai et al. 2006). Fungal Diversity (2020) 103:87–218 Table 10 DNA barcodes available for Ganoderma 127 Species Voucher no ITS rpb2 tef1 Ganoderma adspersum G. angustisporum G. applanatum G. aridicola G. australe G. australe G. austroafricanum G. boninense G. carocalcareus G. casuarinicola G. casuarinicola G. chocoense G. curtisii G. destructans G. ecuadoriense G. eickeri G. ellipsoideum G. enigmaticum G. enigmaticum G. flexipes G. gibbosum G. hoehnelianum G. knysnamense G. leucocontextum G. lingzhi G. lobatum G. lucidum G. lucidum G. martinicense G. mbrekobenum G. mizoramense G. multiplicatum G. multipileum G. mutabile G. nasalanense G. neojaponicum G. orbiforme G. orbiforme G. oregonense G. philippii G. podocarpense G. resinaceum G. ryvardenii G. ryvardenii G. sandunense G. sandunense G. sessile G. shandongense G. sichuanense G. sinense G. steyaertanum GACP15061220 Cui 13817* FIN131R610 Dai 12588* GACP14081671 MFLU 13-0534 CBS138724 WD 2028 DMC 322* Dai 16336* HKAS104639 QCAM3123 CBS 100132 CMW43670* ASL799 CMW49692* GACP14080966* CBS 139792* Dai 15970 Wei 5494 SFC20150630-23 Dai11995 CMW47755* GDGM 40200* Wu 1006-38* JV1212/10J Rivoire 4195 Cui 14404 LIP SWMart08-55* UMN7-3GHA* UMN-MZ4* Dai 13122 CWN 04670 Yuan 2289* GACP17060211* ASI 7032 Cui 13918 GACP14061420 CBS 265.88 E7098 QCAM6422* CBS 194.76 HKAS 58053* HKAS 58054 GACP18012501* GACP18012502 JV 1209/9 Dai 15785 HMAS 42798* Wei 5327 MEL:2382783 MK345425 MG279170 EF060004 KU572491 MH106871 KP142173 KM507324 KJ143905 EU089969 MG279173 MK817650 MH890527 JQ781849 KR183856 KU128524 MH571690 MH106867 KR183855 KU572486 JN383979 KY364264 KU219988 MH571690 KF011548 JQ781858 KF605676 KJ143909 MG279181 KF963256 KX000896 KY643750 KU572488 KJ143913 JN383977 MK345441 JQ520193 MG279186 MK345447 JQ781875 AJ536662 MF796661 KJ143916 HM138671 HM138672 MK345450 MK345451 KF605629 MG279190 JQ781877 KF494998 KP012964 MK371437 MG367507 – – – – – KJ143964 – MG367508 MK840868 – KJ143967 – – – – – MG367513 – – MG367497 – – JX029980 – KJ143969 MG367519 – – – – KJ143972 – – – MG367522 – KJ143974 – – – – – – – – MG367526 – MG367529 – MK371431 MG367563 – KU572502 – MN423152 – KJ143924 – MG367565 MK871328 – KJ143927 – – MH567287 – – KU572496 – – MG367550 MH567287 – JX029976 KU572501 – MG367573 – – – KU572498 KJ143931 – – – MG367576 – KJ143933 – – KJ143934 – – – – KJ143936 MG367580 – KF494976 – 13 128 Table 10 (continued) Fungal Diversity (2020) 103:87–218 Species Voucher no ITS rpb2 tef1 G. steyaertanum G. subresinosum G. thailandicum G. tropicum G. tropicum G. tsugae G. valesiacum G. weberianum G. wiiroense G. williamsianum G. wuzhishanensis G. zonatum 6 WN 20B 7-SU-3-C-70(M)-B HKAS104640* Dai 16434 HKAS 97486 Dai12751b CBS428.84 CBS219.36 UMN-20-GHA Dai 16809 GACP14081689 FL-02 KJ654462 KJ654472 MK848681 MG279194 MH823539 KJ143919 JQ520218 JQ520219 KT952361 MG279183 KU994772 KJ143921 – – MK875831 MG367532 MH883621 KJ143977 – – – MG367535 – KJ143979 – – MK875829 MG367585 – KJ143939 – – – MG367588 – KJ143941 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold Classification—Basidiomycota, Agaricomycotina, Agaricomycetes, Incertaesedis, Russulales, Bondarzewiaceae Type species—Heterobasidion annosum (Fr.) Bref., Unters. Gesammtgeb. Mykol. (Liepzig) 8: 154 (1888) Distribution—North America, Europe, Asia, Australia and Oceania Disease symptoms—There are two Heterobasidion species complexes –H. insulare sensu lato and H. annosum sensu lato—they cause the same symptoms. The H. annosum species complex is one of the major root-rot pathogenic genera of the northern temperate hemisphere (Garbelotto and Gonthier 2013; Kärhä et al. 2018). After the primary infection through stump tops, or stem and root wounds, the taxa can vegetatively infect uninjured trees (secondary infection) by the growth of the mycelium through root contacts (Rishbeth 1950, 1951a, b; Asiegbu et al. 2005; Garbelotto and Gonthier 2013). Heterobasidion could be considered both necrotrophs and saprotrophs; though some species in the H. insulare species complex (e.g. H. austral, H. araucariae) are mainly saprotrophs (Niemelä and Korhonen 1998; Dai and Korhonen 2009; Chen et al. 2014). In contrast to Europe, the pathogenicity of H. annosum sensu lato in China and Japan is uncertain; the complex seems to occur mostly on dead trees, and no symptoms of tree decline are usually visible near infected trees. These observations could be due to different, less intensive forest management strategies in the East-Asian regions, or lack of data on the butt rot symptoms (Dai et al. 2006; Tokuda et al. 2007). The infection causes white pocket rot and heart rot in the roots and the butt of living trees (Korhonen and Stenlid 1998; Asiegbu et al. 2005). Resin, containing mycelium, may also exude from the infected roots, or the bark-scales (Rishbeth 1950). In invaded roots and the basal portions of the trunk, H. annosum sensu lato taxa colonize different plant tissues depending on the host. Heart rot is mainly 13 caused in trees more susceptible to the colonization of the heartwood, e.g. Picea abies. In the case of Pinus, cambium and sapwood are the most severely colonized, while the sapwood of Calocedrus or Sequoiadendron trees is the most colonized (Garbelotto 2004; Asiegbu et al. 2005; Garbelotto and Gonthier 2013). After establishment, the basidiomata of H. annosum sensu lato appear. The localization of the sporocarps is governed by the species, environmental conditions and infection strategy. Some species prefer the root collar for fruiting (H. annosum, H. irregular). Some also produce sporocarps in decay pockets in stumps and fallen trees (H. parviporum, H. abietinum and H. occidentale), or under the intact surface of stumps (H. irregulare, H. occidentale). The sporocarps are sometimes located on the higher parts of the trunk. When moisture is limited, the fungi fruit inside stumps; if the climate is moist and humid, the basidiomata can be found near the ground in the duff at the base of diseased trees. If during primary infection the stump surface is infected, the basidiomata form under an intact top layer. During active pathogenesis, if the standing trees are infected the sporocarps could be found within decay columns in the sapwood (Rishbeth 1950; Otrosina and Garbelotto 2010). The infection kills the functioning sapwood, cambium and heart wood in the roots and at the basal portions of the trunk, resulting in white rot, reduced growth rate, crown dieback (Omdal et al. 2004), and eventually mortality and windthrow of infected trees (Rishbeth 1950; Oliva et al. 2008; Garbelotto and Gonthier 2013). Hosts—The host range of Heterobasidion is extremely wide. The genus has been reported from approximately 200 host species (Korhonen and Stenlid 1998). Taxa mostly occur on gymnosperms, such as Abies, Agathis, Araucaria, Calocedrus, Juniperus, Keteleeria, Larix, Picea, Pinus, Fungal Diversity (2020) 103:87–218 129 Fig. 16 Phylogram of 64 recognized Ganoderma species, obtained from ML of combined ITS, rpb2, and tef1 datasets. Bootstrap values from ML (left) and MP (middle) greater than 70% and BYPP, greater than 0.95, are indicated above the nodes. The tree is rooted with Coriolopsis trogii. Type specimens are indicated in bold Podocarpus, Pseudolarix, Pseudotsuga, Sequoia, Sequoiadendron, Thuja and Tsuga (Buchanan 1988; Corner 1989; Dai and Korhonen 2009; Otrosina and Garbelotto 2010; Garbelotto and Gonthier 2013; Garbelotto et al. 2017). Occasionally, certain Heterobasidion species grow on broadleaved trees of various angiosperm genera (Garbelotto and Gonthier 2013; Ryvarden and Melo 2014). Morphological based identification and diversity There are 33 Heterobasidion epithets listed in Index Fungorum (2020). Of these, eight are related to other polypore genera, based on type studies and morphological observations (Ryvarden 1972, 1985; Buchanan and Ryvarden 1988; Dai and Niemelä1995; Hattori 2003). Besides, the taxonomic status of three further species described from Asia is 13 130 unclear: viz. H. arbitrarium, H. perplexum and H. insulare (Corner 1989; Ryvarden 1989; Stalpers 1996; Hattori 2001; Dai et al. 2002; Tokuda et al. 2009). Given that no sequence data (H. arbitrarium, H. perplexum) or authentic sequences (H. insulare sensu stricto) are available for the molecular resolution, further studies are needed to clarify their status. Formerly, Heterobasidion was considered as a group consisting of only the generic type, H. annosum and H. araucariae and H. insulare (Buchanan 1988; Chase 1989). However, mating studies on Eurasian and North American Heterobasidion collections revealed several intersterile groups, which later became the basis for designating separate taxonomic species within the H. annosum and H. insulare species complexes. Mating experiments revealed three intersterile groups of H. annosum sensu lato in Europe (Korhonen 1978b, Capretti et al. 1990) and two in North America (Otrosina et al. 1993). All intersterile groups have been recognised in the H. annosum species complex are now formally described as separate taxonomic species. European groups were described as H. abietinum, H. parviporum and H. annosum sensu stricto (Niemelä and Korhonen 1998), whereas North American groups were named H. irregulare and H. occidentale (Otrosina and Garbelotto 2010). The mating study by Dai et al. (2002) on Asian “H. insulare” collections revealed three intersterile groups in China, which were subsequently described as Heterobasidion linzhiense (Dai et al. 2007), H. orientale and H. ecrustosum (Tokuda et al. 2009). H. australe related to the H. insulare species complex was also described from China by Dai and Korhonen (2009). Chen et al. (2014) described two further Heterobasidion species (H. amyloideum and H. tibeticum) from the eastern Himalayas based on phylogenetic evidence. These species are morphologically closely related to the members of the H. insulare species complex, but differ in presence of cystidia and amyloid skeletal hyphae in the context. The recently described H. amyloideopsis was collected in the western Himalayas (Pakistan) and formed a monophyletic group with the H. insulare species complex, sister to H. amyloideum (Zhao et al. 2017). The main morphological characters which are used for the identification are the resupinate to pileate basidiocarps, the dimitic hyphal system with mostly simple septate generative hyphae, and the asperulate basidiospores showing no reaction in Melzer’s reagent. Besides morphology, host preference, geographical distribution, and DNA sequence data have also been used for species identification (Otrosina and Garbelotto 2010; Chen et al. 2015a). Molecular based identification and diversity Heterobasidion has been intensely studied by molecular methods. Sequence data are available for the majority of 13 Fungal Diversity (2020) 103:87–218 taxa, and molecular studies were conducted to understand the evolution (Dalman et al. 2010), mating behaviour (Gonthier and Garbelotto 2011), and pathogenicity (Liu et al. 2018a) of Heterobasidion species. Various marker types were used to resolve the phylogeny of the H. annosum species complex, such as isoenzyme (Karlsson and Stenlid 1991a, b), AFLP (Gonthier and Garbelotto 2011) and SSR (Garbelotto et al. 2013) markers. Sequence analyses were carried out initially on nrITS and intergenic spacer regions (Kasuga and Mitchelson 1993a, b; DeScenzo and Harrington 1994), housekeeping genes (Johanesson and Stenlid 2003), peroxidase (Maijala et al. 2003) and laccase genes (Asiegbu et al. 2004), with which it was possible to distinguish four lineages (three European and one North American) within the complex (Asiegbu et al. 2005). Later, allowing the differentiation of a larger number of taxa, further nuclear genes were applied, such as the calmodulin (cam), translation elongation factor 1-α (tef1), glyceraldehydes3-phosphate dehydrogenase (gapdh), heat shock protein (hsp), glutathione-S-transferase (gst1) and transcription factor (tf) genes (Johanesson and Stenlid 2003; Ota et al. 2006; Dalman et al. 2010), as well as two mitochondrial genes, the mitochondrial ATP synthase subunit 6 (ATP6) and mitochondrial rDNA region (Linzer et al. 2008). Dalman et al. (2010) came to the conclusion, that there are two monophyletic sister clades within the H. annosum species complex, representing the Eurasian and North American species. The protein coding largest subunit of RNA polymerase II (rpb1) and the second subunit of RNA polymerase II (rpb2) genes were used by Chen et al. (2014) and were suitable to differentiate Heterobasidion species in the H. insulare species complex. The variability of these markers was confirmed by Chen et al. (2015a) and Zhao et al. (2017) who, among other previously mentioned markers, both used the nuclear large ribosomal subunit (nrLSU) and the mitochondrial small subunit (mtSSU) sequences to their studies (Fig. 18). In this study, we provide a phylogenetic tree (Fig. 19) based on multi-locus phylogenetic analysis of ITS–gapdh–rpb1–rpb2–tef1 sequence data. Sequences of H. arbitrarium and H. perplexum could not be analysed as they are unavailable in GenBank. Furthermore, no sequences are available for the type of H. insulare hence this species was not included in the analysis. The results provide a similar topology to those obtained by Chen et al. (2015a, b) and Zhao et al. (2017). Recommended genetic marker (genus level)—nLSU Recommended genetic markers (species level)—rpb1, rpb2 Accepted number of species –There are 33 epithets in Index Fungorum (2020), however only 15 species are accepted Fungal Diversity (2020) 103:87–218 Table 11 DNA barcodes for accepted species of Golovinomyces 131 Species Strain no ITS LSU Golovinomyces adenophorae G. ambrosiae# G. arabidis G. artemisiae# G. asperifolii G. asperifoliorum G. asterum# G. biocellatus# G. bolayi# G. calceolariae G. chrysanthemi G. cichoracearum# G. circumfusus# G. cucubitarum G. cynoglossi# G. depressus G. echinopis G. euphorbiicola G. fischeri G. glandulariae G. hyoscyami G. inulae G. leuceriae G. longipes# G. macrocarpus G. magnicellulatus# G. monardae# G. montagnei G. neosalviae# G. ocimi G. orontii# G. riedlianus G. reginae G. salviae G. sonchicola# G. sordidus# G. spadiceus# G. tabaci G. valerianae G. verbasci# G. vincae MUMH < JPN_144 MUMH345 HMNWAFU-CF2009256 MUMH175 KUS-F24884 MUMH769 MUMH941 MUMH4293 OLM 35939* MUMH 1934 MUMH853 MUMH623 GLM49501 HMJAU-PM91761 VPRI20429 MUMH696 MUMH1363 MUMH3807 MUMH1345 BRIP 70490* HMNWAFU-CF2013114 MUMH1334 MUMH2527 MUMH2489 HAL 3153* MUMH441* MUMH936 MUMH1082 MUMH4294 MUMH<JPN_:1803 G:00295968 HMNWAFU-CF2012033 BCRU4645 MUMH935 MUMH683 MUMHn41 MUMH<JPN_:3708 BP-1TOB HMNWAFU-CF2011034 MUMH958 MUMH2480 LC516963 AB077642 KR048081 AB077637 MH189697 AB077684 AB769417 AB307671 LC417106 AB430810 AB077654 AB077660 MK452630 MK937796 AB769455 AB077675 AB769414 AB769460 AB769451 NR_166303 KR048155 AB769428 AB246766 AB769440 NR_154105 AB077647 AB307668 AB769413 AB307673 LC306656 LC417099 KR048088 AB246759 AB769437 AB077673 AB077658 LC306664 AF229013 KR048090 AB769468 AB769444 AB077632 AB077641 KR048149 AB077636 MH189696 AB077684 AB769418 AB307671 – AB430810 AB077653 AB077660 MK452703 MK937801 – AB077676 – – AB769452 MN539541 KR048155 – – – – AB077646 AB077691 – – – – KR048157 – AB077690 AB077672 AB077657 – AB022412 KR048159 AB769469 – Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # (Table 12). Amongst these, no sequences are available for H. arbitrarum and H. insulare. Heterobasidion perplexum is not accepted in the genus, pending further studies. References—Dai and Korhonen (2009) (new sp., China, morphology); Tokuda et al. (2009) (new species, East Asia); Dalman et al. (2010) (Evolution, H. annosum species complex, haplotype network); Otrosina and Garbelotto (2010) (new species, North America, biology); Garbelotto and Gonthier (2013) (biology, epidemiology, control); Chen et al. (2014) (new species, China, phylogeny); Chen et al. (2015a) (biogeography, divergence time estimation, phylogeny); Zhao et al. (2017) (new sp., Pakistan, phylogeny). 13 132 Fungal Diversity (2020) 103:87–218 Fig. 17 Phylogram generated from MP analysis based on combined sequences of ITS and LSU sequences of all species of Golovinomyces with molecular data. Related sequences were obtained from GenBank. Fourty-two taxa are included in the analyses, which comprise 1401 characters including gaps, of which 848 characters are constant, 392 characters are parsimony-uninformative and 161 characters parsi- mony-informative. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 927 steps (CI = 0.740, RI=0.699, RC = 0.517, HI = 0.260) in the second tree. The tree was rooted with Neoerysiphe galeopsidis (MUMH 4680). MP bootstrap support value ≥ 50% and BYPP ≥ 0.9 are shown respectively near the nodes. Ex-type strains are in bold 87. Meliola Fr., Syst. orb. veg. (Lundae) 1: 111 (1825) Background Meliola commonly known as “black mildews” or “dark mildews” is the largest genus of Meliolaceae (Hongsanan et al. 2015; Zeng et al. 2017). Fries (1825) established this genus, with the type species M. nidulans. Species in Meliola are mostly biotrophs or pathogens of living leaves and occasionally petioles, twigs, and branches (Hansford 1961; Hosagoudar 1994, 1996, 2008; Mibey and Hawksworth 1997; Old et al. 2003; Hosagoudar and Riju 2013). The phylogenetic placement of Meliola was established by using sequence data from fruiting bodies and placed in Sordariomycetes (Gregory and John 1999; Pinho et al. 2012, 2014, Hongsanan et al. 2015; Justavino et al. 2015). Meliola has been shown to be polyphyletic (Hyde et al. 2020b; Marasinghe et al. 2020; Zeng et al. 2020). There is little sequence data available in GenBank for clarifying relationships between species and establishiing host-specificity (Hongsanan et al. 2015; Zeng et al. 2017). 13 Classification—Ascomycota, Pezizomycotina, Sordariomycetes, Sordariomycetidae, Meliolales, Meliolaceae Type species—Meliola nidulans (Schwein.) Cooke Distribution—commonly found in tropical and subtropical regions (see Zeng et al. 2017) Disease symptoms—Black mildews, forming black, radiate velvety colonies on the surface of plants. Hosts—has a wide range of hosts (see Zeng et al. 2017) Fungal Diversity (2020) 103:87–218 Pathogen biology, disease cycle and epidemiology For pathogen biology, disease cycle and epidemiology see Hongsanan et al. (2015). Morphological based identification and diversity Species in Meliola are characterized by forming web-like colonies on the host surface, hyphal setae developed from superficial hyphae, with hyphopodia, 2–4-spored, unitunicate asci, and 3–4-septate pigmented ascospores (Pinho et al. 2012, 2014; Hongsanan et al. 2015, 2020; Justavino et al. 2015; Hyde et al. 2020a, b; Fig. 20). Cannon and Kirk (2007) reported that the asexual morph of the genus develops from the hypha, form ampuliform hyphopodia or flaskshaped which are called “phialides” (Hongsanan et al. 2015). Conidiogenous cells formed from vegetative hyphae and small, hyaline, unicellular conidia (Cannon and Kirk 2007; Hongsanan et al. 2015). Currently, Meliola comprises over 1700 species (Zeng et al. 2017), which have mostly been introduced by host association, followed by morphology, and disease distribution (Mibey and Hawksworth 1997). Thus, species identification is almost impossible without a host name. However, the same species can be found in different hosts, but it is not clear if this is widespread (Hongsanan et al. 2015). Therefore, testing of host-specificity in Meliola is needed to establish accurate species determination. Molecular based identification and diversity Sequence data of species in Meliola are from direct sequencing of fruiting bodies and fresh mycelium (Pinho et al. 2012, 2014; Hongsanan et al. 2015; Justavino et al. 2015; Hyde et al. 2016, 2020b). LSU and ITS sequence data placed Meliola in Sordariomycetes (Hongsanan et al. 2015, 2020; Maharachchikumbura et al. 2015, 2016; Hyde et al. 2016, 2020a, b). By adding more sequence data, Meliola was shown to be polyphyletic (Marasinghe et al. 2020; Zeng et al. 2020). A phylogenetic tree for Meliola species is presented in Fig. 21. Recommended genetic markers (genus level)—LSU, SSU of nrDNA Recommended genetic marker (species level)—ITS Accepted number of species—There are 3064 epithets listed in Index Fungorum (2020), however only 25 species have DNA molecular data (Zeng et al. 2017, Table 13). References—Cannon and Kirk (2007) (morphology); Pinho et al. (2012, 2014), Hongsanan et al. (2015, 2020), Justavino et al. (2015), Zeng et al. (2020) (morphology and phylogeny) 88. Neoerysiphe U. Braun, Schlechtendalia 3: 50 (1999) Background 133 Neoerysiphe was classified in section Galeopsidis within Erysiphe. Phylogenetic analysis, however, showed Erysiphe to be polyphyletic, and Galeopsidis was raised to generic rank (Takamatsu et al. 1998; Braun 1999; Saenz and Taylor 1999). Therefore, in the current classification Neoerysiphe belongs to the tribe Golovinomyceteae. Classification—Erysiphaceae, Erysiphales, Leotiomycetidae, Leotiomycetes, Pezizomycotina Type species—Neoerysiphe galeopsidis (DC.) U. Braun Distribution—Argentina, Australia, Belarus, Brazil, Bulgaria, Canada, China, Denmark, Finland, France, Germany, Hungary, India, Israel, Italy, Japan, Korea, Netherlands, Norway, Poland, Romania, Russia, Slovakia, Sweden, Switzerland, Turkey, UK, Ukraine and USA (Farr and Rossman 2020). Disease symptoms-powdery mildew Hosts—Neoerysiphe species have a wide host distribution infecting more than 300 species from families including Asteraceae, Acanthaceae, Bignoniaceae, Elaeocarpaceae, Lamiaceae, Rubiaceae and Verbenaceae (Amano 1986; Braun 1999; Bahcecioglu et al. 2006). In general, all species have a specific host range confined to one plant family, except N. galeopsidis which affects several species in four families (Takamatsu et al. 2008). Pathogen biology, disease cycle and epidemiology Discussed under Erysiphaceae. Morphological based identification and diversity Neoerysiphe is in the tribe Golovinomyceteae with Arthrocladiella and Golovinomyces. These genera share a common asexual morph characterized by catenate conidia without distinct fibrosin bodies (Braun 1999). Neoerysiphe is characterized by lobed appressoria and the striate surface of the conidia (Braun 1981; Cook et al. 1997; Braun and Cook 2012). Braun and Cook (2012) mentioned that 15 species of Neoerysiphe are described on different hosts belonging to 11 plant families. Of these 15 species, 11 sexual morphs and 14 asexual morphs have been identified (except N. joerstadii) (Heluta et al. 2010; Braun and Cook 2012). Striatodium is now considered as a synonym of Neoerysiphe and three species viz. N. aloysiae, N. baccharidis and N. maquii were transferred to Neoerysiphe, while Striatodium jaborosae was not transferred as its phylogenetic position are unclear (Wijayawardene et al. 2017a). Molecular based identification and diversity The phylogenetic placement of Neoerysiphe within Erysiphaceae has been reported in a few papers (Saenz and 13 134 Fungal Diversity (2020) 103:87–218 Fig. 18 Members of Heterobasidion annosum species complex. a basidiome on Scots pine, b basidiome on European silver fir, c–e basidiomes on European spruce, f hyphal structure in the trama, g hyphal structure in the context, h–j basidiospores. Scale bars: f, g = 10 µm, h, j = 5 µm Taylor 1999; Mori et al. 2000; Cook et al. 2006). However, these treatments used only limited sequence data for the genus. Takamatsu et al. (2008) conducted the first comprehensive study on this genus using ITS sequence data and the divergent domains D1 and D2 of the 28S rDNA for 30 strains. In their study, the 30 taxa, clustered into three monophyletic groups that were represented by N. galeopsidis on Lamiaceae, N. galii on Rubiaceae and N. cumminsiana from Asteraceae. Takamatsu et al. (2008) used an LSU dataset to estimate the timing of divergence of Neoerysiphe. Neoerysiphe split from other genera ca 35–45 Mya and the three groups of Neoerysiphe diverged between 10 and 15 Mya in the Miocene. Heluta et al. (2010) used 65 ITS sequences in their analyses for identifying Neoerysiphe species infecting Asteraceae and Geranium in Eurasia and introduced three new species, viz. N. hiratae, N. joerstadii and N. nevoi. Gregorio-Cipriano et al. (2020) introduced a new species N. sechii causing powdery mildew on Sechium edule and S. mexicanum in Mexico. The authors mentioned that they were unable to recover DNA in pure form from some samples, as fragments of infected leaves were used during the extraction. Therefore, a specific oligonucleotide for Erysiphales at the 5= region of ITS was designed: ErysiF (5=AGGATCATTACWGAGYGYGAG-3=) was used along with NLP1 (Limkaisang et al. 2006) to amplify a fragment of approximately 1200 bp (that included the ITS1-5.8S-ITS2 region and a section of approximately 680 nucleotides from 13 28S). Species used in the phylogenetic analyses done in this study are listed in Table 14 and given in Fig. 22. Recommended genetic marker (genus level)—ITS and LSU Recommended genetic markers (species level)—ITS Accepted number of species—There are 16 species epithets in Index Fungorum (2020), for 15 accepted species. However, only 12 species have DNA sequence data (N. chelones, N. gnaphalii and N. rubiae do not have molecular data) (Table 14). References—Takamatsu et al. (1998), Braun (1999), Saenz and Taylor (1999) (morphology); Heluta et al. (2010), Braun and Cook (2012), Gregorio-Cipriano et al. (2020) (morphology and phylogeny). 89. Nothophoma Qian Chen & L. Cai, Stud. Mycol. 82: 212 (2015) Background Nothophoma was introduced by Chen et al. (2015b) by transferring five Phoma species. Species are saprobes and pathogens. In addition, to the phytopathogens, N. gossypiicola has been isolated from clinical samples of humans in the respiratory secretion of a patient with pneumonia and a human bronchial wash sample (Valenzuela-Lopez et al. 2018). Chethana et al. (2019) showed that the comparative pathogenicity of Nothophoma species is low when compared to other opportunistic pathogens. Some species grow on other fungi or occur in soil (Boerema et al. 2004; Fungal Diversity (2020) 103:87–218 135 Fig. 19 Phylogram generated from ML analysis based on combined ITS, rpb1, rpb2, gapdh and tef1 sequence data of Heterobasidion species. Related sequences were obtained from GenBank. Fourty-four strains are included in the analyses, which comprised 4314 characters including gaps. The tree was rooted with Bondarzewia occidentalis (HHB 14803) and B. tibetica (Cui 12078). Tree topology of the ML analysis was similar to the Bayesian analysis. ML bootstrap values ˃ 50% and BYPP ˃ 0.80 are shown respectively near the nodes Aveskamp et al. 2009; 2010; Chen et al. 2015b). Some Nothophoma species might be host-specific to a single plant genus or family (Aveskamp et al. 2010; Chen et al. 2015b). However, there is no study of host-specificity in Didymellaceae. Abdel-Wahab et al. (2017) identified 55 bioactive compounds from an endophyte, N. multilocularis. Of these, ten compounds showed strong antimicrobial activity in combination. Distribution—Argentina, China, Italy, India, Korea, Netherlands, Spain, Tunisia, Ukraine, United States Disease symptoms—brown spot of fruits, leaf spots, shoot canker, stem cankers Leaf spot produced by Nothophoma anigozanthi is elliptical to circular and black. Nothophoma pruni and N. quercina develop small, dark red or purple pinpoint lesions (Chethana et al. 2019). Liu et al. (2018b) identified N. quercina infection on ornamental crab-apple. Symptoms on the trunk appear as warts, the periderm around warts can become cracked, and the bark is roughened with a scaly periderm. During dry weather, these cankers expand and coalesce (Liu et al. 2018b; Fig. 23). Nothophoma quercina develops shoot Classification—Ascomycota, Pezizomycotina, Dothideomycetes, Pleosporomycetidae, Pleosporales, Didymellaceae Type species—Nothophoma infossa (Ellis & Everh.) Qian Chen & L. Cai 13 136 Table 12 DNA barcodes for accepted species of Heterobasidion Fungal Diversity (2020) 103:87–218 Species Strain Heterobasidion abietinum 00057/2 00051/1 PFC 5247 PFC 5373 H. amyloideopsis MS 8848* M 118 H. amyloideum Li 1878* Li 1675 Li 1883 H. annosum K 06125/2 K 06071/1 PFC 5252 PFC 5260 H. araucariae 65008 CBS 743.94* PFC 5434 H. australe K 05175/2 K 04167/4 K 04164/3 H. ecrustosum K 05168/1 K 07103/2 PFC 5438 H. irregulare 57001/VE 05025/VE PFC 5398 PFC 5288 H. linzhiense Dai 5408* Cui 7216 MSM 0097 H. occidentale 79034/VE 98005/VE PFC 5362 PFC 5388 H. orientale K 97011/7 K 03293/2 K 00085/2 H. parviporum K 04121/3 08123/VE PFC 5262 Dai 5537* H. tibeticum Dai 5468 Dai 5534 ITS rpb1 rpb2 gapdh tef1 KJ651453 KJ651450 KC492895 KC492956 KT598384 KT598385 KJ651455 KJ651454 KJ651456 KJ651459 KJ651458 KC492906 KC492911 KJ651462 MH862503 KX130098 KJ651467 KJ651465 KJ651464 KJ651468 KJ651471 KX130099 KJ651473 KJ651478 KP863586 KP863575 KJ651484 KJ651480 MH233930 KJ651485 KJ651489 KP863584 KP863585 KJ651490 KJ651493 KJ651492 KJ583212 KJ651500 KC492957 KJ651507 KJ651505 KJ651506 KJ651632 KJ651629 – – – – KF033157 KF033155 KF033156 KF453492 KF453491 – – KJ651636 – – KF033137 KF033135 KF033134 KF033142 KF033145 – KJ651638 KJ651643 – – KF033154 KF033148 – KJ651645 KJ651649 – – KF033141 KF033140 KF033139 KF453493 KF453495 – KF033153 KF033151 KF033152 KJ651725 KJ651722 – – KT598388 KT598389 KF006538 KF006534 KF006537 KF453498 KF453497 – – KJ651729 – – KF006506 KF006502 KF006500 KF006513 KF006517 – KJ651731 KJ651736 – – KF006533 KF006524 – KJ651738 KJ651742 – – KF006512 KF006510 KF006508 KF453499 KF453501 – KF006531 KF006527 KF006529 KJ651756 KJ651753 KP863657 KP863664 – – KJ651758 KJ651757 KJ651759 KJ651762 KJ651761 KP863659 KP863661 KJ651766 – KX130104 KJ651771 KJ651769 KJ651768 KJ651772 KJ651775 KX130105 KJ651777 KJ651782 KP863652 KP863641 KJ651788 KJ651784 – KJ651789 KJ651793 KP863650 KP863651 KJ651794 KJ651797 KJ651796 KJ651800 KJ651805 KP863662 KJ651812 KJ651810 KJ651811 – – KC571636 KC571687 – – – – – – – KC571646 KC571651 – – KX130101 – – – – – KX130102 – – KP863616 KP863606 – – – – – KP863614 KP863615 – – – – – KC571688 – – – Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold necrosis, stem browning, and wilted leaves on Chaenomeles sinensis (Yun and Oh 2016). In Tunisia, shoot blights caused by N. quercina were observed with diffuse cankers with gummosis on buds (Triki et al. 2019). 13 Hosts— Has a wide range of hosts including Anigozanthos flavidus, Anigozanthus maugleisii, Arachis hypogaea, Chaenomeles sinensis, Gossypium sp., Fraxinu spennsylvanica, Malus micromalus, Microsphaera alphitoides, Olea europaea, Phellodendrona murense, Pistacia vera, Prunu Fungal Diversity (2020) 103:87–218 137 Fig. 20 Morphology of Meliola species a Meliola thailandicum on Dimocarpus longan. b Meliola sp. on Citrus reticulata. c Meliola sp. on Citrus maxima. d Colony on the host surface. e Hyphopodia on mycelium. f Section through ascoma. g Peridium. h Setae. i Young ascus. j Mature ascus. k, l Ascospores. Scale bars: f=50 μm, g, i–l=30 μm, h=10 μm and e=5 μm savium, Prunus dulcis, Spiraea salicifolia, Quercus sp. and Ziziphus jujube (Babaahmadi et al. 2018; Chen et al 2015b, 2017; Chethana et al. 2019; Jianyu et al. 2016; Liu et al. 2018b; Moral et al. 2017, 2018; Soleimani et al. 2018; Triki et al. 2019; Valenzuela-Lopez et al. 2018; Yun and Oh 2016; Zhang et al. 2020). Morphological based identification and diversity This genus was introduced by Chen et al. (2015b) based on molecular data to delineate a more natural classification for the Ascochyta-Didymella-Phoma species complex (Chen et al. 2015b; Fig. 23). Species produce elongate, barrel-shaped, olivaceous brown chlamydospores in chains (Chen et al. 2015b). However, there is little morphological variation among species (Valenzuela-Lopez et al. 2018). Molecular based identification and diversity Species identification is based on multi-locus sequence phylogeny. Phylogenetic analyses of combined LSU, ITS, tub2 and rpb2 sequence data resulted in several new species being added to this genus by Chen et al. (2015b), AbdelWahab et al. (2017), Valenzuela-Lopez et al. (2018), Chethana et al. (2019), Marin-Felix et al. (2019) and Zhang et al. 13 138 Fungal Diversity (2020) 103:87–218 Fig. 21 Phylogram generated from RAxML analysis based on combined ITS and LSU sequence data of Meliola species. Related sequences were obtained from GenBank. Thirty-five strains are included in the analyses, which comprised 1655 characters includ- ing gaps. The tree was rooted with Chaetosphaeria innumera (SMH 2748). Tree topology of the ML analysis was similar to the Bayesian analysis. ML bootstrap values ≥ 50% and BYPP ≥ 0.90 are shown respectively near the nodes (2020). Here we provide an updated phylogenetic tree for this genus (Fig. 24). 90. Phellinus Quél., Enchir. fung. (Paris): 172 (1886) Background Phellinus was introduced by Quélet (1886) with P. igniarius (≡ Boletus igniarius) as its type species (Murrill 1903) and is placed in Hymenochaetaceae (He et al. 2019). Traditionally, most poroid Hymenochaetaceae were placed in Phellinus, which has been characterized by a dimitic hyphal system and perennial habit of the basidiomata (Gilbertson 1979; Larsen and Cobb-Poulle 1990; Ryvarden and Gilbertson 1994; Núñez and Ryvarden 2000). However, phylogenetic studies revealed that the morphologically defined Phellinus sensu lato had polyphyletic origins within the Hymenochaetoid clade, and most species previously classified as Phellinus are now members of various segregate genera (e.g. Wagner and Fischer 2001, 2002; Jeong et al. 2005; Dai 2010; Rajchenberg et al. 2015; Drechsler-Santos et al. 2016). According to the most narrowly defined generic concept, Phellinus sensu stricto is limited to the P. igniarius species complex (Fischer and Binder 2004), which includes species causing a delignifying trunk rot mostly on various Recommended genetic markers (genus level)—LSU, ITS Recommended genetic markers (species level)—tub2, rpb2 Since the colony morphology and other morphological features in Didymellaceae often overlap, initial species identification is recommended with LSU and ITS sequence data using all type species in Didymellaceae. Once the genus is identified as Nothophoma, the phylogenetic analysis could be done with LSU, ITS, tub2, and rpb2 sequence data. Accepted number of species—There are 12 species in Index Fungorum (2020) with DNA sequence data (Table 15). References—Chen et al. (2015b), Abdel-Wahab et al. (2017), Valenzuela-Lopez et al. (2018), Chethana et al. (2019), Marin-Felix et al. (2019), Zhang et al. (2020) (morphology and phylogeny) 13 Fungal Diversity (2020) 103:87–218 Table 13 DNA barcodes available for Meliola 139 Species Culture/specimen number LSU ITS Meliola aristolochiae-tagalae M. brachyodonta M. caesalpiniicola M. centellae M. citri-maximae M. clerodendricola M. crescentiae M. danielliae M. jasmini-sambac M. lithocarpigena M. monnieriae M. mucunicola M. niessleana M. panici M. peruiferae M. pistaciicola M. pottsiae M. puerariae M. pseudosasae M. schimigena M. tamarindi M. trichostroma M. variaseta M. vernaliae MFLU 16-0088* VIC32066 VIC32061 VIC31244* MFLU 14-0288* MFLU 13-0620* VIC32056 VIC32057 MFLU 17-1044* MFLU 13-0628* VIC32062 MFLU 15-0386 UBC F23799 VIC32063 VIC 31249* MFLU 16-0070* MFLU 13-0631* MFLU 16-0087* MFLU 16-2136 MFLU 17-1048* MFLU 14-C0282 VIC32068 DRJ 54 (PMA) VIC 31240 MN747479 MN747473 KC618644 KC618641 NG042650 KX458474 KT021647 KC618649 KC618648 MN747482 MN747474 KC618647 KT157533 KC833049 KC618651 NG 060294 MN747478 MN747475 MN747472 KX845434 MN747484 KP744489 KC618643 EF094840 JX096808 MN747479 – – – NR137799 – – – – MN747482 MN747474 – KT157534 – – – MN747478 MN747475 – – MN747484 – – – – Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*) deciduous trees in temperate areas (Brazee 2015; Zhou et al. 2016). Based on a wider generic concept, several morphologically similar species described from East Asia, Africa or America are considered as part of Phellinus sensu stricto (Decock et al. 2006; Yombiyeni et al. 2011; Cui and Decock 2013; Bian et al. 2016; Campos-Santana et al. 2016; Vlasák and Vlasák 2017; Salvador-Montoya et al. 2018; Zhu et al. 2018). In this study, we follow the broader concept of classification of Phellinus sensu stricto, pending further studies. Classification—Agaricomycotina, Basidiomycota, Agaricomycetes, Incertae sedis, Hymenochaetales, Hymenochaetaceae Type species—Phellinus igniarius (L.) Quél., Enchir. fung. (Paris): 177 (1886) Distribution—If the wider generic concept of Phellinus were accepted it would be a globally distributed genus, with certain species found in East Asia, Europe, North America (Dai 2010; Cui and Decock 2013; Brazee 2015; Zhou et al. 2016; Vlasák and Vlasák 2017; Zhu et al. 2018), Central- and South America (Decock et al. 2006; Campos-Santana et al. Table 14 DNA barcodes available for Neoerysiphe Species Strain no ITS LSU Neoerysiphe aloysiae N. baccharidis N. cumminsiana N. galeopsidis N. galii N. geranii BCRU 04878 BCRU 01609 VPRI 20387 MUMH 4680 MUMH 4682 HMNWAFUCF2013083 MUMH 3442 MUMH 4668 DAR 33493 MUMH 2460 MUMH 4671 AB329683 AB329685 GU356539 AB498949 AB498951 KR048092 – AB329684 – AB022369 AB103365 KR048161 AB498962 AB498976 GU356546 AB329686 AB498975 – – – – – N. hiratae N. joerstadii N. kerribeeensis N. maquii N. nevoi Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold strains and voucher 13 140 Fungal Diversity (2020) 103:87–218 Fig. 22 Phylogram generated from MP analysis based on combined sequences of ITS and LSU sequences of all species of Neoerysiphe with molecular data. Related sequences were obtained from GenBank. 12 taxa are included in the analyses, which comprise 2023 characters including gaps, of which 1790 characters are constant, 167 characters are parsimony-uninformative and 66 characters parsimonyinformative. The parsimony analysis of the data matrix resulted in the maximum of four equally most parsimonious trees with a length of 316 steps (CI = 0.848, RI=0.678, RC = 0.575, HI = 0.152) in the first tree. Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted with Golovinomyces adenophorae (MUMH144). MP bootstrap support value ≥ 50% and BYPP ≥ 0.9 are shown respectively near the nodes. Ex-type strains are in bold 2016; Salvador-Montoya et al. 2018) and Africa (Yombiyeni et al. 2011; Cloete et al. 2016). However, the members of the P. igniarius species complex are known only from the Northern Hemisphere (Brazee 2015; Zhou et al. 2016). Disease symptoms—Members of Phellinus produce white rot, decaying polysaccharides and delignifying the substrata (Niemelä 1974, 1977; Ryvarden and Gilbertson 1994; Wagner and Fischer 2002; Decock et al. 2006; Cui and Decock 2013; Brazee 2015; Cloete et al. 2016, de CamposSantana et al. 2016). The rot could be localized in the trunk as a column of decay (Brazee 2015), in both fallen and in standing dead trunks (Niemelä 1977; Campos-Santana et al. 2016). Branches of living trees (Niemelä 1974; Decock et al. 2006), dead, fallen, corticated branches and logs (Niemelä 1972) and dead stumps (Niemelä 1972; Decock et al. 2006; Campos-Santana et al. 2016) are colonized and decayed. The fungus penetrates the heartwood, causing heartrot (Niemelä 1974; Larsson et al. 2006), sometimes extending into the sapwood (Niemelä 1977; Larsson et al. 2006). Decay characteristics (i.e. colour, fragility and fragmentation) vary between species (Niemelä 1972, 1974, 1977; Yombiyeni et al. 2011; Luna et al. 2012; Campos-Santana et al. 2016). Pathogenic species, such as P. tremulae or P. resupinatus are usually associated with other basidiomycete species, pathogenic bacteria and basal fungi (Kallio 1972; Cloete et al. 2016). Phellinus tremulae is a common and harmful pathogen of aspen (Populus species), penetrating the heartwood along dead branches (Niemelä 1974), but is also capable of spreading through the sapwood (Larsson et al. 2006), forming conks around the decayed tissues (Jones 1998; Fig. 25). Phellinus resupinatus is also a factor of Esca disease, causing white rot and decline of the cordons in vineyards (Cloete et al. 2016), besides other symptoms caused by this disease (Jayawardena et al. 2019a). Hosts—Most species in the P. igniarius species complex are specialized to a single or few angiosperm genera (Fischer and Binder 1995; Zhou et al. 2016), and only P. piceicola has been reported from gymnosperms (Cui and Dai 2012). Species of the P. igniarius species complex have been recorded from various host genera, such as Acer, Alnus, Arctostaphylos, Betula, Carpinus, Fagus, Fraxinus, Laburnum, Picea, Populus, Prunus, Salix, Sorbus and Tilia (Tomšovský et al. 2010; Brazee 2015; Zhou et al. 2016). The members of other Phellinus sensu stricto lineages are known from several additional angiosperm genera, such as Artemisia, Astronium, Caesalpinia, Carya, Castanopsis, Dimorphandra, Minquartia, Morus, Sacaglottis, Schinopsis, Quercus and Vitis (Lombard and Larsen 1985; Decock et al. 2006; Yombiyeni et al. 2011; Cui and Decock 2013; 13 Fungal Diversity (2020) 103:87–218 Fig. 23 Nothophoma quercina on Malus micromalus a Malus micromalus (Crab-Apple tree). b Canker on the trunk. c, d appearance of conidiomata on trunk. e longitudinal section through conidiomata. f 141 cross-section of conidiomata g, h conidiogenous cells. i, j conidia. k upper view on PDA. l reverse view on PDA. Scale bars: d=1000 μm e, f = 50μm g–j 10 μm 13 142 Fungal Diversity (2020) 103:87–218 Fig. 24 Phylogram generated from maximum likelihood analysis based on combined LSU, ITS, tub2 and rpb2 sequence data of Nothophoma species. Related sequences were obtained from GenBank. Seventeen strains are included in the combined sequence analyses. Phoma herbarum (CBS 615.75) and Vacuiphoma bulgarica (CBS 357.84) was used as the outgroup taxa. The best scoring RAxML tree with a final likelihood value of − 5537.646741 is presented. The matrix had 284 distinct alignment patterns, with 12.23% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.238395, C = 0.241637, G = 0.276596, T = 0.243371; substitution rates AC = 0.975188, AG = 4.004775, AT = 1.500008, CG = 0.519461, CT = 10.843965, GT = 1.000000; gamma distribution shape parameter a = 1.764918. ML bootstrap support value ≥ 50% and BYPP ≥ 0.95 are shown respectively near the nodes. Extype strains are in bold de Campos-Santana et al. 2016; Vlasák and Vlasák 2017; Salvador-Montoya et al. 2018). Morphological based identification and diversity Phellinus in a wider sense is morphologically heterogenous. The main features of the P. igniarius species complex are the crusted pileal surface (except resupinate species), the hymenial setae arising from the subhymenium (except specimens of “P. pseudoigniarius”, see Dai and Yang 2008; Zhou et al. 2016), and the colourless, inamyloid, indextrinoid and weakly cyanophilous basidiospores (Wagner and Fischer 2001; Dai 2010; Zhou et al. 2016). In many cases, the species separation in the complex is difficult when solely based on morphological characters (Sell 2008). Host preference is 13 also widely used for delimiting species (Tomšovský et al. 2010). Similar to members of the P. igniarius species complex, other Phellinus species also have perennial basidiomata, but differ in having distinctive macroscopical features (e.g. size and shape of pores, rimose surface, cracked basidiocarps, absence of pileus crust, see Dai et al. 2008; Bian et al. 2016; Cloete et al. 2016; Vlasák and Vlasák 2017) or microscopic characteristics (e.g. hyphal structure, the shape of setae, basidiospore reaction in chemical solutions). For example, P. bicuspidatus is unique in having a monomitic hyphal system with short bicuspid setae (Lombard and Larsen 1985; Cloete et al. 2016). Members of the P. ellipsoideus group are Fungal Diversity (2020) 103:87–218 Table 15 DNA barcodes available for Nothophoma 143 Species Isolate LSU ITS tub2 RPB2 Nothophoma anigozanthi N. arachidis-hypogaeae N. brennandiae CBS 381.91* CBS 125.93 CBS 145912* JW 1066 CBS 377.67 UTHSC:DI16-294 CBS 123395 * CBS 140674 * AUMC-12003* MFLUCC 18–1600 * MFLUCC18–1601 CBS 633.92 UTHSC:DI16-270 MCC 1082 * CFCC 53928* CFCC 53929 UTHSC: DI16-285* GU238039 GU238043 MN823430 MN823429 GU238079 LN907437 GU238089 LN880537 KY996744 MH827028 MH827026 EU754127 LN907413 – MN737828 MN737829 LN907428 GU237852 GU237771 MN823579 MN823578 GU237845 LT592943 FJ427025 LN880536 – MH827007 MH827005 GU237900 LT592929 MF664467 MN737833 MN737834 LT592939 GU237580 GU237583 MN824753 MN824752 GU237611 LT593012 FJ427135 LN880539 – MH853671 MH853669 GU237609 LT592998 MF664468 MN879295 MN879296 LT593008 KT389655 KT389656 MN824604 MN824603 KT389658 LT593082 KT389659 LT593073 – MH853664 MH853662 KT389657 LT593067 – MN879292 MN879293 LT593078 N. gossypiicola N. infossa N. macrospora N. multilocularis N. pruni# N. quercina# N. raii N. spiraeae N. variabilis Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # well-characterised by their weakly dextrinoid basidiospores and hooked hymenial setae (Zhu et al. 2018). There are several “Phellinus” species which have been described solely on morphological features. The status of these species should be critically re-evaluated based on molecular evidence. Amongst these, certain species (e.g. P. deuteroprunicola, P. eugeniae, P. formosanus, P. livescens, P. prunicola, P. setulosus, P. tenuiculus, P. wahlbergii) may belong to Phellinus sensu stricto (Gilbertson 1979; Chang 1995; Chang and Chou 1999, 2000; Robledo et al. 2003; Wang et al. 2011; Rajchenberg et al. 2015; Campos-Santana et al. 2016), but further studies are required to confirm their placements. Molecular based identification and diversity In early molecular studies, the restriction fragment length polymorphism (RFLP) data of enzymatically amplified rDNA was used by Fischer (1995) to study the taxonomy of P. igniarius and its closest relatives in Europe. Later, single nuclear genes (ITS, Fischer and Binder 2004), or combined datasets (ITS-tef1, Tomšovský et al. 2010; Zhou et al. 2016) were used to investigate the species boundaries and phylogenetic relationships within the P. igniarius species complex. Phylogenetic analyses by Brazee (2015) used ITS, LSU, tef1 and rpb2, with isolates representing 13 species-level lineages in the complex. Zhou et al. (2016) distinguished 15 species, five of which are described as new from China and the USA. Based on our multigene analysis (Fig. 26), 16 species can be found in the P. igniarius species complex, distributed throughout the Northern Hemisphere. Amongst these, ten species are known from eastern Asia, eight from Europe and seven from North America. Phellinus caribaeo-quercicola was the first species described from the “P. ellipsoideus group” based on molecular evidence (Decock et al. 2006). The nLSU-based phylogenetic analysis of Decock et al. (2006), have shown that P. caribaeo-quercicola grouped close to the P. igniarius species complex and some other Phellinus species (viz. P. bicuspidatus, P. chaquensis and P. spiculosus). Later molecular taxonomic studies used combined datasets of various nuclear markers. The combined analyses of nITS, nLSU, tef1 and rpb2 have confirmed the phylogenetic position of P. caribaeo-quercicola and five morphologically similar species have been accepted in Phellinus sensu stricto (Yombiyeni et al. 2011; Cui and Decock 2013; Campos-Santana et al. 2016; Zhu et al. 2018). Currently, this later group consists of six species and mostly has tropical or subtropical distributions (Zhu et al. 2018). Recommended genetic marker (genus level)—LSU Recommended genetic markers (species level)—ITS, tef1, rpb2 Accepted number of species—There are 479 epithets listed in Index Fungorum (2020. However, most of the species belong to other poroid Hymenochaetaceae genera, such as Fomitiporia, Fomitiporella, Fulvifomes, Fuscoporia, 13 144 Fungal Diversity (2020) 103:87–218 Fig. 25 Phellinus igniarius. a causing white-rot decay on willow b–d basidiomes on living willow e, f hymenial setae g tramal skeletal hyphae h basidiospores, Scale bars: e–h = 10 µm Nothophellinus, Phellinidium, Phellinopsis, Phellinotus, Phellopilus, Phylloporia, Porodaedalea, Sanghuangporus and Tropicoporus (Wagner and Fischer 2001, 2002; Niemalä et al. 2001; Dai 2010; Drechsler-Santos et al. 2016; Rajchenberg et al. 2015; Zhou et al. 2016). Based on molecular data, 30 species are accepted in Phellinus sensu stricto, from among 16 species in the P. igniarius species complex (Table 16; Fig. 26). References—Tomšovský et al. (2010) (phylogeny, P. igniarius species complex, Europe), Brazee (2015) (phylogeny, P. igniarius species complex, North America), Zhou et al. (2016) (phylogeny, P. igniarius species complex), Zhu et al. (2018) (phylogeny, P. ellipsoideus group) 91. Pseudoseptoria Speg., Anal. Mus. nac. B. Aires, Ser. 3 13: 388 (1910) [1911] Background Spegazzini (1910) introduced Pseudoseptoria as an asexual genus typified with Pseudoseptoria donacicola. Wijayawardene et al. (2012) placed the genus under Ascomycota, genera incertae sedis. Quaedvlieg et al. (2013) placed the genus in Dothioraceae and this was accepted by Thambugala et al. (2014). With LSU sequence data, Crous et al. (2017) placed Pseudoseptoria to Saccotheciaceae. Wijayawardene et al. (2017a, b, 2018, 2020) accepted this placement. Species of Pseudoseptoria are recorded as pathogens on Poaceae (Quaedvlieg et al. 2013), impairing the photosynthetic process resulting in yield loss. 13 Classification—Ascomycota, Pezizomycotina, Dothideomycetes, Dothideomycetidae, Dothideales, Saccotheciaceae Type species—Pseudoseptoria donacicola Speg. Distribution—Australia, Canada, India, Italy, New Zealand, Poland, Russia, UK and USA (Dennis1986; Ginns 1986; French 1989; Pennycook 1989; Merezhko 1991; Cunnington 2003; Mulenko et al. 2008; Kamal 2010; Farr and Rossman 2020). Disease symptoms—halo spot, leaf blotch and stem speckle Halo spot: Elliptical, tan to brownish-grey spots (<10mm long) with a dark border surrounded by a prominent yellow halo that can be observed on the leaf blade, sometimes covering the entire leaf blade. In older lesions, small pycnidia may be visible (Slopek and Labun 1992; Carmona et al. 1996; Murray et al. 2013). Leaf blotch: Brown flecks and frog-eye spots on leaf blades can be observed in early spring, which enlarges to straw-coloured blotches scattered with minute pycnidia. These spots may drop out, leaving holes (Horst 2013). Stem speckle: The disease occurs in the leaves, sheaths, culms, and head spikes. The lesions are rectangular, ash white, (1-2 mm long) with a brown, thin border. The lesion is delimited by leaf veins and becomes distinct with a clear boundary. The conidia formed on the lesions disperse by wind and rain. Pathogen biology, disease cycle and epidemiology The pathogen is dispersed through spores in rain splash. Infection requires an extended period of wetness. Spore Fungal Diversity (2020) 103:87–218 germination and infection occur optimally at temperatures between 15 and 25 °C. Spores produced in overwintering crop debris serve as sources of primary inocula (Sinclair and Dhingra1995). Further studies are needed regarding the disease mechanisms and disease cycle. Hosts—members of Poaceae are susceptible: Alopecurus pratensis, Arrhenatheru melatius, Arundo donax, Bromus species, Dactylis glomerata, Danthonia spicata, Elymus alaskanus, Festu carubra, Hordeum vulgare, Panicum virgatum, Phleum species, Phragmites australis and Poa species (Ginns 1986; Pennycook 1989; Shivas1989; Greuter et al. 1991; Merezhko 1991; Roane and Roane 1996; Gravert and Munkvold 2002; Mulenko et al. 2008; Farr and Rossman 2020) Morphological based identification and diversity The genus is characterized by immersed, branched, septate, pale brown mycelium, pycnidial, solitary or linearly aggregated, immersed, brown, globose, unilocular, thinwalled conidiomata of walls of pale brown cells of textura angularis with distinct, central, circular ostioles. Conidiogenous cells are discrete, determinate or indeterminate, hyaline, smooth, ampulliform with a prominent cylindrical papilla and falcate. Conidia are fusoid, hyaline, aseptate, guttulate, smooth and thin-walled, and acutely rounded at each end (Sutton 1980; Quaedvlieg et al. 2013). Molecular based identification and diversity Quaedvlieg et al. (2013) revised the Septoria and septoria-like genera based on morphology and multi loci analyses and introduced two new species. Phylogenetic analysis conducted by Crous et al. (2017) was based only on LSU sequence data. In our analysis, we used LSU, ITS and rpb2 and obtained the same topology (Fig. 27). Recommended genetic marker (genus level)—LSU Recommended genetic markers (species level)—LSU, ITS and rpb2 Accepted number of species—There are eight epithets listed in Index Fungorum (2020). However, only three species have DNA sequence data (P. collariana, P. donacis and P. obscura) (Table 17). References—Sutton (1980) (morphology); Quaedvlieg et al. (2013), Crous et al. (2017) (morphology and phylogeny) 92. Stemphylium Wallr., Flora Cryptogamica Germaniae 2: 300 (1833) Background Stemphylium mainly comprises saprobes or weak plant pathogens (Woudenberg et al. 2017). However, some species are primary pathogens causing leaf blight on various crops, resulting in yield and economic losses (Hanse et al. 2015; Brahmanage et al. 2018). The asexual morph is a 145 dematiaceous hyphomycete while the sexual morph was previously defined as Pleospora sensu stricto (Inderbitzin et al. 2009; Woudenberg et al. 2017). Rossman et al. (2015) recommended the use of Stemphylium over Pleospora which has been followed by various authors (Hongsanan et al. 2017, 2020; Wijayawardene et al. 2018, 2020). Stemphylium is one of the most important moulds human allergens in the USA (Gutiérrez-Rodríguez et al. 2011). Brahmanage et al. (2018) discussed the pathogenicity, disease severity, distribution and molecular phylogenetic affinities of pathogenic isolates of Stemphylium. Stemphylium leaf blight caused by S. versicarum was identified as an emerging disease in New York, USA. Sharma et al. (2020b) provided two genome resources for two S. versicarum isolates from leaf blight of onion. Genomic data allows for an understanding of the population biology, fungicide resistance, as well as development of control strategies against the disease. Pathogenesis related 511 secreted proteins were predicted from S. lycopersici by Zeng et al. (2018) which helps in understanding the roles of proteins in host penetration and tissue necrosis. Stemphylium loti secretes Tenuazonic acid, inhibiting the plant plasma membrane H+-ATPase, which results in membrane potential depolarization and eventually necrosis (Bjørk et al. 2019). Su et al. (2019) fine-mapped the tomato grey spot resistance gene Sm, in a 185kb region through a map-based cloning strategy. Leach et al. (2020) identified a relationship between thrips (Thrips tabaci) and S. vesicarium in the development of Stemphylium leaf blight in onion. Classification—Ascomycota, Pezizomycotina, Dothideomycetes, Pleosporomycetidae, Pleosporales, Pleosporaceae Type species—Stemphylium botryosum Wallr. Distribution—worldwide Disease symptoms—Gray spot, Stemphylium leaf blight (Leaf spot, defoliation, curling and bending of the leaf margins and stems) Initial symptoms of the leaves are small, irregular, brown spots. Generally, the spots gradually lighten and eventually become greyish as they become necrotic and dry. When severe, yellow spots can be seen throughout all leaves of the plant and the heavily infected leaves die (Basallote-Ureba et al. 1999, Crous et al. 2016; Brahmanage et al. 2018). Hosts—Species are pathogenic on a wide range of hosts including Amaryllidaceae, Asparagaceae, Fabaceae, Malvaceae, Poaceae, Rosaceae and Solanaceae Pathogen biology, disease cycle and epidemiology Species can survive as saprobes on crop residues, soil, plant debris and on many alternative hosts and ascospores become the primary inocula in the following season. Once the disease is established during favourable conditions, conidial production in primary lesions may occur, dispersing 13 146 13 Fungal Diversity (2020) 103:87–218 Fungal Diversity (2020) 103:87–218 ◂Fig. 26 Phylogram generatedfrom RAxML analysis based on com- bined ITS, LSU, Tef1-α and rpb2 sequence data of Phellinus species. Related sequences were obtained from GenBank. Fifty-five strains are included in the analyses, which comprised 3170 characters including gaps. The tree was rooted with Phellinopsis conchata (DLL2009-149 and L-7601). Tree topology of the ML analysis was similar to the Bayesian analysis.ML bootstrap values >50% and BYPP >0.80% are shown respectively near the nodes spores to healthy plants by wind and rain splashing. Environmental factors such as temperature and moisture are key factors in disease development. Seedlings of plants can transmit the diseases if they become infected in the nursery (Basallote-Ureba et al. 1998, 1999; Boshuizen et al. 2004; Zheng et al. 2010; Blancard 2012). However, to date, diseases and epidemiology such as factors affecting the disease development, interactions with different hosts and genetics of host resistance are poorly studied (Das et al. 2019). Morphological based identification and diversity Species can be distinguished from other hyphomycetes in Pleosporaceae forming phaeodictyospores, based on percurrent proliferation of its conidiophores and apically swollen conidiogenous cells (Köhl et al. 2009). Simmons (1967) established criteria for morphological identification of various Stemphylium species and introduced Pleospora herbarum as the sexual morph of the type species Stemphylium botryosum. However, Simmons (1985) subsequently reclassified and reported Pleospora tarda as the sexual morph of Stemphylium botryosum and Pleospora herbarum as the sexual morph of Stemphylium herbarum (Moslemi et al. 2017). Morphological features, such as size and time of pseudothecial maturation, conidiophores and conidia and ascospore shape and size can be considered as important characteristics in species identification (Câmara et al. 2002; Fig. 28). Köhl et al. (2009) and Woudenberg et al. (2017) pointed out that the lack of (ex-) type material of species and morphology-based species identifications without molecular evidence make it difficult in determining correct species nomenclature. Therefore, relying on morphological characters alone in identifying species is not recommended. Molecular based identification and diversity ITS (rDNA) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) sequences were used by Câmara et al. (2002) to confirm the monophyly of Stemphylium. In the extensive study of 110 Stemphylium strains from various hosts and DNA sequence data of ITS, gapdh and tef1 loci and the intergenic spacer between vmaA and vpsA, Inderbitzin et al. (2009) identified 23 representatives derived from type strains, while 40 strains remained unnamed. Woudenberg 147 et al. (2017) revised the genus and accepted 28 species, synonymizing 22 names and proposing two new combinations based on combined analyses of the ITS, gapdh and cmdA gene regions. Marin-Felix et al. (2019) introduced three new species (S. rombundicum, S. truncatulae and S. waikerieanum), while Brahmanage et al. (2018) introduced S. dianthi based on multi loci phylogeny. In this study, we reconstruct the phylogeny based on combined ITS, gapdh and cmdA sequence data (Fig. 29). Recommended genetic marker (genus level)—ITS Recommended genetic markers (species level)—cmdA, gapdh Accepted number of species—There are 207 epithets listed in Index Fungorum, however only 32 species have DNA sequence data (Table 18). References—Simmons (1967), Köhl et al. (2009) (morphology); Câmara et al. (2002), Inderbitzin et al. (2009), Moslemi et al. (2017), Woudenberg et al. (2017), Brahmanage et al. (2019), Marin-Felix et al. (2019) (morphology and phylogeny) 93. Thyrostroma Höhn., Sitzungsberichte der Kaiserlichen Akademie der Wissenschaften Math.-naturw. Klasse Abt. I 120: 472 (1911) Background Thyrostroma belongs to Dothidotthiaceae of Pleosporales in Dothideomycetes, Ascomycota (Hongsanan et al. 2020). Thyrostroma was established by Höhnel (Höhnel 1911) and is typified by T. compactum. Thyrostroma had been treated as a synonym of Coryneum, Stegonsporium, Stigmina, and Thyrococcum, Thyrostromella and Wilsonomyces (Höhnel Höhnel 1911; Morgan-Jones 1971; Sutton and Pascoe 1989; Sutton 1997; Index Fungorum 2020). Thyrostroma has been reported as the asexual morph of Dothidotthia based on the production of a hyphomycete state in culture (Ramaley 2005), however, there is no phylogenetic evidence to support this link. With new morphological information and phylogenetic analyses, Thyrostroma and Dothidotthia species were retained in separate genera (Crous et al. 2016; Marin-Felix et al. 2017; Senwanna et al. 2019). Thyrostroma species are pathogens, saprobes or endophytes associated with canker, dieback and leaf spots in terrestrial habitats (Yuan and Old 1990; Marin-Felix et al. 2017; Senwanna et al. 2019). Species of Thyrostroma have been recorded from various plants, however, host-specificity and pathogenic capacity of Thyrostroma has not yet been clarified. Classification—Ascomycota, Pezizomycota, Dothideomycetes, Pleosporomycetidae, Pleosporales, Dothidotthiaceae 13 148 Table 16 DNA barcodes available for Phellinus Fungal Diversity (2020) 103:87–218 Species Strain ITS LSU tef1 rpb2 Phellinus alni FP-134638-Sp KU139167 KU139213 KU139330 KU139280 P. alni BRNM 714865 GQ383730 – GQ383840 – P. amazonicus MUCL 53036* KU499940 KU376305 KU936772 – P. amazonicus MUCL 51478 KU499929 KU376294 KU936769 – P. arctostaphyli FP-94186-R KU139145 KU139252 KU139350 KU139266 P. arctostaphyli FP-94140-R KU139143 KU139250 KU139348 KU139264 P. artemisiae JV 1603/1-J* KY230518 KY230518 – – P. austrosinensis Dai 13680a* – KP027474 – – P. betulinus NJB2009-FpG KU139153 KU139248 KU139368 KU139311 P. betulinus FP-105325-Sp KU139154 KU139239 KU139369 KU139312 P. bicuspidatus CBS 427.86* MH861982 MH873674 – – P. caribaeo-quercicola MUCL 46004* HM635698 DQ127280 HM635726 – P. caribaeo-quercicola MUCL 46003 HM635697 DQ127279 HM635725 – P. castanopsidis CUI 10153* JQ837944 JQ837956 KU936783 – P. castanopsidis CUI 10157 JQ837945 JQ837957 KU936784 – P.chaquensis MUCL 46742 – DQ122396 – – P.chaquensis CTES568170 MG242440 MG242445 – – P. ellipsoideus MUCL 47867 KU954545 KU954540 KU936786 – P. ellipsoideus MUCL 45929 KU954544 DQ127283 KU936785 – P. gabonensis MUCL 52025* HM635708 HM635690 HM635731 – P. gabonensis MUCL 52007 HM635718 HM635685 HM635729 – P. igniarius BRNM 714889 GQ383709 – GQ383791 – P. igniariusa *Yang 67 JQ828880 – KR013111 – P. igniarius CCBAS575 LN714586 – – LN714693 P. laevigatus NJB2011-PLa1-F KU139148 KU139241 KU139372 KU139305 P. laevigatus BRNM 714867 GQ383778 – GQ383856 – P. lundellii NJB2011-PLu-F KU139185 KU139234 KU139337 KU139300 P. lundellii NJB2011-GR1 KU139182 KU139232 KU139336 KU139301 P. monticola Dai 5413* JQ828889 – KR013087 – P. monticola Cui 10482 JQ828888 – KR013086 – P. mori Dai 8309/Dai 8310 FJ627259 HQ328535 – – P. nigricans NJB2011-PA1-F KU139169 KU139222 KU139340 KU139297 P. nigricans FP-62186-T KU139176 KU139227 KU139343 KU139290 P. orientoasiaticus Cui 9753* JQ828926 – KR013079 – P. orientoasiaticus Cui 9727 JQ828921 – KR013076 – P. padicola Cui 2257* JQ828905 – KR013073 – P. padicola Cui 2414 JQ828906 – – – P. parmastoi Dai 12558* JQ828900 – KR013089 – P. parmastoi TN-6432 KU139158 KU139245 KU139376 – P. piceicola Cui 10440* JQ828908 – – – P. piceicola Cui 10455 JQ828910 – KR013085 – P. pomaceoides JV 1403/4-J* KR013069 – KR013107 – P. pomaceoidesb SRM-158-Sp KU139140 KU139210 KU139353 KU139267 P. pomaceus TN-449 KU139142 KU139254 KU139352 KU139263 P. pomaceus MJ 44/07 GQ383783 – GQ383858 – P. populicola TN-526* KU139179 KU139231 KU139333 KU139303 P. populicola JV 0110/21 KR013062 – KR013093 – P. resupinatus STE-U 7769* KM523246 KM523251 – – P. spiculosus CBS 345.63* MH858307 MH869918 – – P. tremulae NJB2011-PT1-F KU139132 KU139201 KU139357 KU139276 P. tremulae FP-135202-T KU139134 KU139207 KU139359 KU139271 P. turbinatus JV 1407/73-J KT156687 – – – P. vietnamensis Cui 16434* – MG867716 MG867722 MG867719 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold 13 a as P. pseudoigniarius b as PhellinusNA2 Fungal Diversity (2020) 103:87–218 149 Fig. 27 Phylogenetic tree generated by maximum likelihood analysis of combined LSU, ITS and rpb2 sequence data. Fourteen strains are included in the analyses, which comprised 2207 characters including gaps. The tree was rooted with Elsinoe veneta (CBS 164.29) and Elsinoe phaseoli (CBS165.31). Tree topology of the ML analysis was similar to the BYPP analysis. The best scoring RAxML tree with a final likelihood value of − 7330.368152 is presented. The Table 17 DNA barcodes available for Pseudoseptoria Species Isolate Pseudoseptoria collariana P. donacis# P. obscura CBS 135104* KF251721 CBS 313.68 CBS 135103 LSU ITS rpb2 KF251218 KF252223 MH870852 MH859141 KF251722 KF251219 KF252224 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # matrix had 500 distinct alignment patterns, with 29.98% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.250948, C = 0.235140, G = 0.278289, T = 0.235623; substitution rates AC = 2.242594, AG = 3.171649, AT = 1.699638, CG = 1.459509, CT = 8.754890, GT = 1.000000; gamma distribution shape parameter α = 0.601361 ML bootstrap values ≥ 65% and BYPP ≥ 0.90 are shown respectively near the nodes Type species—Thyrostroma compactum (Sacc.) Höhn Distribution—Australia, Iran, Korea, Russia, USA, Uzbekistan Disease Symptoms—Thyrostroma canker, dieback and leaf spots (Fig. 30a, b) Hosts—Pathogens of Acanthophyllum sp., Astragalus sp., Capparis parvifiora, Celtis occidentalis, Cornus officinalis, Echinops sp., Elaeagnus angustifolia, Ephedra equisetina, Eucalyptus mannifera subsp. maculosa, Franseria sp., Halimodendron halodendron, Lycium barbarum, Morus alba, Robinia pseudoacacia, Sambucus caerulea, Styphnolobium 13 150 japonicum, Tilia cordata, Ulmus pumila (Farr and Rossman 2020). Morphological based identification and diversity Thyrostroma species can be differentiated using conidial dimensions and septation in aged conidia and molecular phylogeny (Crous et al. 2016; Marin-Felix et al. 2017; Senwanna et al. 2019; Fig. 30). Senwanna et al. (2019) reported the sexual morph of Thyrostroma in T. ulmicola for the first time. The sexual morph is characterized by pseudothecial, immersed, erumpent or superficial, uniloculate or multiloculate ascostromata, globose to subglobose ascomata, a two-layered peridium, bitunicate, clavate asci, fusiform to ellipsoidal, 1-septate, ascospores. Molecular based identification and diversity In the past, there has been no comprehensive phylogenetic study in Thyrostroma and consequently, its taxonomy was and still is mostly based on morphological characters. Based on LSU sequence data, Thyrostroma clustered in a wellsupported clade within the Dothidotthiaceae (Marin-Felix et al. 2017; Crous et al. 2019). The asexual morph and sexual morph relationship were resolved by Senwanna et al. (2019) by molecular evidence. To achieve correct generic and species identification and taxonomic placement, phylogenetic studies using LSU, SSU, ITS, and tef1 were performed (Senwanna et al. 2019). This study reconstructs the phylogeny using a combined LSU, SSU, ITS, and tef1 sequence dataset (Fig. 31). The topology is in accordance with Marin-Felix et al. (2017), Senwanna et al. (2019) and Hyde et al. (2020b). Recommended genetic marker (genus level)—LSU Recommended genetic markers (species level)—ITS, tef1, rpb2 and tub2 LSU, ITS and tef1 are the common genetic markers used in the identification of Thyrostroma species. Combined LSU, SSU, ITS and tef1 genes provide a satisfactory resolution for resolving species. Based on the comparison of ITS and tef1gene regions, most species in Thyrostroma are not significantly different from one another, therefore, Senwanna et al. (2019) suggested that rpb2, tub2 are reliable genes for distinguishing species within Thyrostroma. Accepted number of species—There are 27 epithets in Index Fungorum (2020), however only 13 species have DNA sequence data (Table 19). References—Höhnel (1911), Yuan and Old (1990), Ramaley (2005) (morphology); Marin-Felix et al. (2017), Crous et al. (2016, 2019), Senwanna et al. (2019) (morphology and phylogeny). 13 Fungal Diversity (2020) 103:87–218 94. Wojnowiciella Crous, Hern.-Restr.& M.J. Wingf., Persoonia 34, 201 (2015) Background Wojnowiciella was introduced by Crous et al. (2015) to include Wojnowiciella eucalypti which exhibited somewhat similar morphological characteristics to Wojnowicia, such as setose pycnidia, with ampulliform, enteroblastic, phialidic conidiogenous cells, but differed with apapillate conidiomata lacking setae and having dark brown conidia. Classification—Ascomycota, Pezizomycota, Dothideomycetes, Pleosporales, Phaeosphaeriaceae Type species—Wojnowiciella eucalypti Crous, Hern.-Restr. & M.J. Wingf Distribution—Australia (Hernandez-Restrepo et al. 2016), China (Crous et al. 2015, Giraldo et al. 2017), Colombia (Crous et al. 2015, Giraldo et al. 2017), New Zealand (Crous et al. 2019), South Africa and Western Cape (Crous et al. 2016) Disease symptoms—Leaf spots Most species are reported as saprobes with the exception of Wojnowiciella cissampeli, W. eucalypti and W. vibruni which were isolated from leaves and twigs of Cissampelos capensis, Eucalyptus and Viburnum utile respectively (Hernandez-Restrepo et al. 2016). Their pathogenicity or disease symptoms are not indicated clearly and there is a need to establish pathogenicity of these species. Hosts—Cissampelos capensis, Dactylis sp., Eucalyptus grandis, Rosa sp., Leptocarpus sp., Lonicera sp., Spartium sp. and Viburnum utile (Farr and Rossman 2020). Morphological based identification and diversity Wojnowiciella was introduced to include species that were phylogenetically distinct but morphologically similar to Wojnowicia (Crous et al. 2015). Wojnowiciella is characterized by apapillate conidiomata without setae and dark brown conidia. Some species of Wojnowiciella also produce hyaline microconidia. Karunarathna et al. (2017) first reported the sexual morph of W. dactylidis. Phookamsak et al. (2019) transferred Wojnowicia rosicola to Wojnowiciella rosicola based on morphology and phylogenetic analyses. Molecular based identification and diversity Wojnowiciella is a well-supported genus in the family Phaeosphaeriaceae (Phookamsak et al. 2019). A combined multiloci phylogeny of LSU, SSU, tef1 and ITS is used in placing species of Wojnowiciella within Phaeosphaeriaceae. To identify species within the genus ITS, LSU, rpb2 and tef1 are used (Marin-Felix et al. 2019; Phookamsak et al. 2019). Here we provide an updated phylogenetic tree for this genus (Fig. 32). Fungal Diversity (2020) 103:87–218 151 Fig. 28 Stemphylium sp. a Ascomata on host b Vertical section through an ascoma c immature and mature asci d Pseudoparaphyses e Ascospores f Ascospores in Indian ink. Scale bars: b = 50 μm, c–f = 10 μm Recommended genetic markers (genus level)—LSU Recommended genetic markers (species level)—ITS, rpb2, tef1 Accepted number of species—Nine species are accepted with molecular data (Table 20). References—Crous et al. (2015), Karunarathna et al. (2017), Marin-Felix et al. (2019), Phookamsak et al. (2019) (morphology and phylogeny) Updated genera The following genera are updated due to the addition of many new species during recent years. 95. Cladosporium Link, Mag. Gesell. naturf. Freunde, Berlin 7: 37 (1816) [1815] Cladosporium Link, Mag. Gesell. naturf. Freunde, Berlin 7: 37 (1816) [1815] 13 152 Fungal Diversity (2020) 103:87–218 Fig. 29 Phylogram generated from MP analysis based on combined sequences of ITS, gapdh and cmdA sequences of all species of Stemphylium. Related sequences were obtained from GenBank. Thirty three taxa are included in the analyses, which comprise 1936 characters including gaps, of which 1355 characters are constant, 271 characters are parsimony-uninformative and 310 characters parsimonyinformative. The parsimony analysis of the data matrix resulted in the maximum of four equally most parsimonious trees with a length of 1112 steps (CI = 0.660, RI=0.721, RC = 0.476, HI = 0.340) in the first tree. Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted with Alternaria abundance (CBS 534.83). MP bootstrap support value ≥ 50% and BYPP ≥ 0.9 are shown respectively near the nodes. Ex-type strains are in bold Background Cladosporium belongs to Cladosporiaceae in the order Capnodiales (Hyde et al. 2013). Established in 1816 with C. herbarum as type species, Cladosporium is one of the largest genera of dematiaceous hyphomycetes. Davidiella was erected by Braun et al. (2003) to accommodate the sexual morph of Cladosporium sensu stricto. Davidiella was therefore recognized as a synonym of Cladosporium as Cladosporium has priority over Davidiella at generic rank, and is also the more commonly used name in literature (Bensch et al. 2012). Therefore, Cladosporiaceae took preference over Davidiellaceae (Bensch et al. 2012). Cladosporium species have a worldwide distribution and can be easily spread in the environment, because of their small conidia. Cladosporium includes many important pathogens causing leaf spots and stem rots of many plant hosts. For example, Cladosporium fulvum is the causal agent of tomato leaf mold (van Kan et al. 1991). Cladosporium species have been recorded as endophytes and may have a positive effect, for example, C. sphaerospermum was isolated from the roots of Glycine max which can promote its growth (Hamayun et al. 2009). Some species, such as C. herbarum, are also known as common contaminants in clinical laboratories and cause allergic lung disease (de Hoog et al. 2000). Several species were also isolated from human respiratory samples (Sandoval-Denis et al. 2016). Thirteen species are fungicolous (Heuchert et al. 2005; Sun et al. 2019) and have the potential for biological control in agriculture and forestry (Torres et al. 2017). There have been studies towards understanding the genetic components of Cladosporium. Cladosporium fulvum is an important model species in the plant pathology study. 13 Fungal Diversity (2020) 103:87–218 Table 18 DNA barcodes available for Stemphylium 153 Species name Isolate/specimen no ITS gapdh cmdA Stemphylium amaranthi S. armeriae S. astragali # S. beticola# S. botryosum# S. callistephi S. canadense S. chrysanthemicola# S. dianthi S. drummondii S. eturmiunum# S. gracilariae S. halophilum S. ixeridis S. lancipes S. loti S. lucomagnoense S. lycii S. lycopersici S. majusculum S. novae-zelandiae S. paludiscirpi S. rombundicum S. sarciniforme S. simmonsii# S. solani# S. symphyti S. trifolii S. triglochinicola S. truncatulae S. vesicarium# S. waikerieanum CBS 124746* CBS 338.73 CBS 116583* CBS 141024* CBS 714.68* CBS 527.50* CBS 116602* CBS 117255* MFLU 19-0556* CBS 346.83* CBS 109845* CBS 482.90* CBS 337.73* CBS 124748* CBS 133314* CBS 407.54* CBS 116601* CBS 125241* CBS 122639* CBS 717.68* CBS 138295* CBS 109842* BRIP 27486* CBS 110049* CBS 133518* CBS 116586* CBS 115268* CBS 116580* CBS 718.68* BRIP 14850* CBS 715.68* VPRI 21969* KU850505 KU850511 KU850512 KU850520 KC584238 KU850539 KU850641 KU850640 MK500718 GQ395365 KU850541 KU850549 KU850553 KU850590 KU850596 KU850597 KU850629 KU850602 KU850611 KU850618 KU850631 KU850620 MK336819 KU850591 KU850637 KU850627 KU850643 KU850647 KU850648 MK336815 KU850565 MK336832 KU850652 KU850658 KU850659 KU850667 AF443881 KU850686 KU850782 KU850781 – KU850687 KU850689 AF443883 KU850700 KU850737 KU850742 KU850743 KU850770 KU850748 KU850756 AF443891 KU850772 KU850762 MK336865 KU850738 KU850778 KU850768 KU850784 KU850788 KU850789 MK336861 KU850712 MK336878 KU850793 KU850799 KU850800 KU850808 KU850826 KU850828 KU850932 KU850931 MK500734 KU850829 KU850831 KU850839 KU850843 KU850881 KU850887 KU850888 KU850920 KU850893 KU850902 KU850909 KU850922 KU850911 MK336842 KU850882 KU850928 KU850918 KU850934 KU850938 KU850939 MK336838 KU850855 MK336855 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # Iakovidis et al. (2020) reported classical mapping strategies for loci of tomato that response to sequence-monomorphic effector Ecp5. Convergent evolution could be used for choosing different functional genes according to individual plant breeding needs. Ge et al. (2019) showed that Cladosporium species have the potential to be used in industrial processes. They identified a new glucose oxidase gene CtgoxB from C. tianshanense and suggested this could be a candidate for the aquatic feed and detergent industries. Transcriptome and proteome analyses of C. fulvuim showed that 14 out of 59 predicted proteases are expressed during in vitro and in planta, of which nine belong to serine proteases and the rest belong to metallo and aspartic proteases (Jashni et al. 2019). This study also confirmed the presence of six proteases at proteome level during the infection. Grinn-Gofroń et al. (2019) developed and evaluated the models of forecasting possibilities of airborne spore concentrations in 18 sites in six countries across Europe. The study revealed the possibility of reliable prediction of fungal spore levels using gridded meteorological data. They concluded that these forecasting models can be used in the more timely and efficient management of phytopathogenic and of human allergic diseases. An environmentally isolated strain of C. sphaerospoermum substantially enhanced plant growth, early flowering and increase in crop yield after exposure in vitro (Li et al. 2019). Pan et al. (2020) identified four new hybrid polyketides (Cladosin L-O) from C. shaerospermum which showed strong cytotoxicity, antifungal activity and moderate antibacterial activity. 13 154 Fungal Diversity (2020) 103:87–218 Fig. 30 a, b Symptoms on Ulmus pumila caused by Thyrostroma ulmicola (MFLU 16-1622); c, d Sporodochia on the host surface. e Section of sporodochium. f Conidiogenesis and conidiogenous cells. g–l Conidia. m Germinated conidium. Scale bars: d = 1000 µm, e = 200 µm, f–m = 30 µm Classification: Ascomycota, Pezizomycotina, Dothideomycetes, Pleosporomycetidae, Capnodiales, Cladosporiaceae Type species–Cladosporium herbarum (Pers.) Link Distribution– Worldwide Disease symptoms–Leaf spots, leaf blight, discolourations, necrosis, or shot-hole symptoms, on stems and fruits, rots Hosts– Cladosporium species occur on a wide range of host plants including Asparagaceae, Asteraceae, Fabaceae, Myrtaceae, Orchidaceae, Poaceae, Solanaceae and Vitaceae (Farr and Rossman 2020). Some species can be hyperparasites of insects and fungi (Heuchert et al. 2005; Islam et al. 2019; Sun et al. 2019; Abdel-Baky 2000). These species can cause allergies in humans such as sneezing, hives and also can cause eye, ear and sinus infections (de Hoog et al. 2000). 13 Pathogen biology, disease cycle and epidemiology Cladosporium survives in the soil or on plant debris and produce spores during humid weather. Fungal spores germinate under high humidity and cool to warm temperatures. Wind, rain and irrigation splash, workers, tools, and insects readily disseminate spores (Jordan et al. 1990; Lan and Scherm 2003; Liu et al. 2019). Fungal Diversity (2020) 103:87–218 155 Fig. 31 Phylogenetic tree generated by maximum likelihood analysis of LSU, SSU, ITS and tef1 sequence data of Thyrostroma species. Related sequences were obtained from GenBank. The tree was rooted with Dothidotthia robiniae (MFLUCC 16-1175), D. symphoricarpi (CPC 12929) and Wilsonomyces carpophilus CBS 147.36). Tree topology of the ML analysis was similar to the Bayesian analysis. The best scoring RAxML tree with a final likelihood value of − 5556.187049 is presented. The matrix had 170 distinct alignment patterns, with 18.30% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.243922, C = 0.240705, G = 0.270231, T = 0.245142; substitution rates AC = 3.570314, AG = 6.771467, AT 4.177691, CG = 1.603201, CT = 31.935571, GT = 1.000000; gamma distribution shape parameter α = 0.602378. Maximum likelihood bootstrap support values greater than 60% and Bayesian posterior probabilities ≥ 0.95 (BYPP) are indicated above the nodes. Ex-type (ex-epitype) and voucher strains are in bold Morphological based identification and diversity The asexual morph of Cladosporium species is characterized by a unique coronate structure of the conidiogenous loci and conidia, consisting of the central convex dome surrounded by a raised periclinal rim (Bensch et al. 2012; Fig. 33), while ascomata of sexual morphs are identical to those of Mycosphaerella (sect. Tassiana) (Braun et al. 2003). Historically, all types of dematiaceous hyphomycetes with amero- to phragmosporous conidia formed in acropetal chains had been assigned to Cladosporium sensu lato, resulting in the complication to resolve a natural classification of Cladosporium. Various mycologists proposed natural genetic circumscriptions of Cladosporium (David 1997; Braun et al. 2003; Aptroot 2006). David (1997) found the unique structure of conidiogenous loci and conidial hila using scanning electron microscopy. Based on the genetic circumscriptions, some cladosporioid groups, such as Fusicladium being non-coronate (Schubert et al. 2003), have been excluded from Cladosporium s. str. Various Cladosporium species have been re-examined based on the new generic concepts (Schubert and Braun 2004, 2005a, b, 2007; Schubert 2005; Schubert et al. 2006; Braun and Schubert 2007; Braun et al. 2008). A polyphasic approach revealed three major species complexes within Cladosporium, viz. C. cladosporioides, C. herbarum and C. sphaerospermum (Schubert et al. 2007; Dugan et al. 2008; Bensch et al. 2010; Bensch et al. 2015). A modern monograph of the genus treated 993 names of Cladosporium sensu lato, of which 169 were recognized in Cladosporium sensu stricto and others remain doubtful (Bensch et al. (2012). Molecular based identification and diversity The first molecular examination of Cladosporium-like hyphomycetes based on ITS and SSU was carried out by Braun et al. (2003), who confirmed the strong heterogeneity. A new genus Davidiella was established to accommodate the sexual morphs of Cladosporium sensu stricto species which were previously assigned in Mycosphaerella. Aptroot (2006) made a better circumscription of Davidiella after he found species of Davidiella have ascospores with irregular cellular inclusions, which are absent in Mycosphaerella. Schoch et al. (2006) studied the phylogenetic relationships 13 156 Table 19 DNA barcodes available for Thyrostroma Fungal Diversity (2020) 103:87–218 Species Isolate/Voucher no LSU SSU ITS tef1 Thyrostroma compactum T. cornicola T. ephedricola T. franseriae CBS 335.37 CBS 141280* MFLUCC 18-1125* CBS 487.71* CBS 700.70 MFLUCC 18-0787 MFLUCC 16-1186* MFLU 16-1795* MFLUCC 16-1170* MFLUCC 18-1191* MFLUCC 16-1160* MFLUCC 16-1176 MFLUCC 16-1178* MFLUCC 16-1180 MFLUCC 16-1188 MFLUCC 16-1172* MFLUCC 16-1173 MFLUCC 16-1163 MFLUCC 16-1711 MFLUCC 16-1166* MFLUCC 16-1164 KY905664 KX228300 MK765854 KX228301 KX228302 MK765857 MK751822 MK751823 MK751824 MK751825 MK751826 MK751827 MK751828 MK751829 MK751830 MK751840 MK751841 MK751834 MK751839 MK751846 MK751845 _ _ MK765853 _ _ MK765858 MK751767 MK751768 MK751769 MK751770 MK751771 MK751772 MK751773 MK751774 MK751775 MK751785 MK751786 MK751779 MK751784 MK751791 MK751790 KY905670 KX228248 MK765855 KX228249 KX228250 MK765856 MK751732 MK751733 MK751734 MK751735 MK751736 MK751737 MK751738 MK751739 MK751740 MK751750 MK751751 MK751744 MK751749 MK751756 MK751755 KY905681 KX228372 _ KY905680 KY905682 _ MK908022 MK908023 MK908024 MK908025 MK908026 MK908027 MK908028 MK908029 MK908030 MK908040 MK908041 MK908034 MK908039 MK908046 MK908045 T. jaczewskii T. celtidis T. moricola T. lycii T. robiniae T. styphnolobii T. tiliae T. ulmicola T. ulmigenum Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold of 96 taxa of the Dothideomycetes using LSU, SSU, tef1 and rpb2 gene data. Davidiella and its Cladosporium asexual morphs were assigned to the family Cladosporiaceae in the order Capnodiales, together with Mycosphaerellaceae. Crous et al. (2007) delimited Cladosporium from morphologically similar genera using their morphology and DNA phylogeny based on LSU. Several species were transferred to new genera such as Hyalodendriella, Ochrocladosporium, Rachicladosporium, Rhizocladosporium, Toxicocladosporium and Verrucocladosporium. Furthermore, C. castellanii was confirmed as a synonym of Stenella araguata, while the type species of Stenella resided in Teratosphaeriaceae instead of Mycosphaerellaceae. Schubert et al. (2007) performed a comprehensive study of the C. herbarum species complex based on both morphology and phylogenetic analysis with five combined genes. Bensch et al. (2010) carried out species and ecological diversity within the C. cladosporioides species complex. More than 200 isolates belonging to the C. cladosporioides species complex were examined and analyzed on the basis of ITS, actand tef1 gene regions. A comprehensive monograph of Cladosporium sensu lato was provided by Bensch et al. (2012) based on morphology and combined ITS, act and tef1 sequence data. In their study, 993 names assigned to Cladosporium sensu lato are treated and 169 names were recognized in Cladosporium sensu stricto. Bensch et al. (2015) introduced the three major species 13 complexes in Cladosporium, i.e. C. cladosporioides, C. herbarum and C. sphaerospermum, and 19 new species were described. Razafinarivo et al. (2016) introduced a new species C. lebrasiae from milk bread rolls in France, Ma et al. (2017) introduced six new soil-inhabiting Cladosporium species from plateaus in China. Bensch et al. (2018) studied Cladosporium species from indoor environments and introduced 16 new species. Several new Cladosporium species including Cladosporium omanense (Halo et al. 2019), C. passiflorae and C. passifloricola (Rosado et al. 2019) have been introduced more recently. In this study, we reconstruct the phylogeny of Cladosporium based on ITS, tef1 and act sequenced data (Table 21; Fig. 34). Recommended genetic marker (genus level)—ITS and LSU Recommended genetic markers (species level)—act and tef1 (in a few cases tub2) Accepted number of species–There are 844 epithets listed in Index Fungorum (2020), however, 138 species have DNA sequence data. References–David (1997), Aptroot (2006), Schubert and Braun (2004, 2005a, b, 2007), Schubert (2005), Schubert et al. (2006), Braun and Schubert (2007), Braun et al. (2008) (morphology), Braun et al. (2003), Schoch et al. (2006), Bensch et al. (2010, 2012, 2015), Ma et al. (2017) (morphology and phylogeny) Fungal Diversity (2020) 103:87–218 Fig. 32 Phylogram generated from MP analysis based on combined sequences of ITS, LSU and tef1 sequences of all the accepted species of Wojnowiciella. Related sequences were obtained from GenBank. Ten taxa are included in the analyses, which comprise 2460 characters including gaps. Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted with Galiicola baoshanensis (HKAS102234). The best scoring RAxML tree with a final likeli- 157 hood value of − 6772.195394 is presented. The matrix had 261 distinct alignment patterns, with 0.96% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.230657, C = 0.279364, G = 0.252128, T = 0.237852; substitution rates AC = 1.388608, AG = 2.845402, AT = 2.389715, CG = 0.838197, CT = 7.220493, GT = 1.000000; gamma distribution shape parameter a = 0.650385. ML and MP bootstrap support value ≥ 50% are shown respectively near the nodes. Ex-type strains are in bold 13 158 Fungal Diversity (2020) 103:87–218 Table 20 Details of Wojnowiciella, isolates used in the phylogenetic analyses Species Isolates ITS LSU tef1 References Wojnowiciella cissampeli W. dactylidis W. eucalypti W. kunmingensis W. leptocarpi W. lonicerae W. rosicola W. spartii W. viburni CBS 141297* MFLUCC 13-0735* CBS 139904* KUMCC18-0159* CBS 115684* MFLUCC 13-0737* MFLUCC 15-0128* MFLUCC 13-0402* MFLUCC 12-0733* KX228272 KP744470 KR476741 MK356380 KX306775 KP744471 MG828979 KU058719 KC594286 KX228323 KP684149 KR476774 MK356354 KX306800 KP684151 MG829091 KU058729 KC594287 LT990616 – LT990617 MK359071 LT990615 – – – – Crous et al. (2016) Liu et al. (2015) Crous et al. (2015) Phookamsak et al. (2019) Hernandez-Restrepo et al. (2016) Liu et al. (2015) Phookamsak et al. (2019) Li et al. (2015) Wijayawardene et al. (2013) Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold Fig. 33 Cladosporium cladosporioides. a Conidiomata. b, c, e Macro- and micronematous conidiophores and conidia chains. d. Secondary ramoconidia. f. Conidia. Scale bars: b, c, e, f = 50 µm, d–g=10 µm 96. Colletotrichum Corda, in Sturm, Deutschl. Fl., 3 Abt. (Pilze Deutschl.) 3(12): 41 (1831) Background Colletotrichum was introduced by Corda (1831), belonging to Glomerellaceae (Glomerellales, Sordariomycetes), and is the sole member of this family (Maharachchikumbura et al. 2015, 2016; Hyde et al. 2020b). Species may occupy different lifestyles, ranging from necrotrophy to hemibiotrophy as well 13 as endophytism (Crouch et al. 2014). Colletotrichum species are important plant pathogens in both tropical and temperate regions on many economically important crops (Hyde et al. 2009a, b, 2014; Cannon et al. 2012; Jayawardena et al. 2016b, c). Based on recognized scientific and economic importance this genus was voted the eighth most important plant pathogenic group in the world (Dean et al. 2012). Colletotrichum species have been identified as endophytes (Manamgoda Fungal Diversity (2020) 103:87–218 et al. 2013; Tao et al. 2013; Hyde et al. 2014; Jayawardena et al. 2016c) and some are saprobes on dead plant material (Photita et al. 2005; Jayawardena et al. 2016b). A few species have been identified to be pathogenic to humans (C. coccodes, C. dematium, C. gloeosporioides (Natarajan et al. 2013)) and on insects (C. fioriniae (Damm et al. 2012b)). Colletotrichum species are cosmopolitan in distribution and show a diverse hosts association (Sharma et al. 2015). A host plant genus can be infected by many Colletotrichum species (Silva et al. 2012; Jayawardena et al. 2016c), and on the contrary, a single species of Colletotrichum can infect many host plants (Damm et al. 2012a, b; Weir et al. 2012). Correct species identification is important to understand the species diversity, plant pathology and quarantine, concerning human infections, agriculture, bio-control, plant breeding, whole-genome sequencing, developing and maintaining knowledge databases, bioprospecting and understanding the evolutionary history (Jayawardena et al. 2016a). Due to a small number of distinctive morphological characters available for identification, misidentification of these species is frequent. Misapplication and misidentification of species are also due to the misunderstanding of their host-specific nature, ambiguous species boundaries and incorrect sequences (Cannon et al. 2012; Hyde et al. 2014; Jayawardena et al. 2016a). Therefore, having a stable taxonomy for the identification of these species is a significant practical concern (Shenoy et al. 2007). To establish a natural classification system, researchers strongly recommend the use of geographical, ecological, morphological and genetic data (Cai et al. 2009; Sharma and Shenoy 2016). Species of Colletotrichum are extensively studied as model organisms (Cannon et al. 2012; Hyde et al. 2014). This enables the researchers to understand the pathogen variation, infection mechanism, evolution and population dynamics. Pathogenicity genes of C. graminicola, C. higginsianum and C. orbiculare have been studied (Huser et al. 2009; O’Connell et al. 2012). Asakura et al. (2009) discovered the importance of the pexophagy factor ATG26 for appressorium formation. A total of 28 genome projects that include 25 different Colletotrichum species can be found; 15 of these strains are still at the annotation stage and 13 are now at the ‘Fungal Standard Draft’ stage (Carbú et al. 2019). These genomes will allow further analysis of species diversity and evolutionary mechanisms and may serve as a foundation for genetic analysis that leads to a greater understanding of interactions between plants and fungal pathogens (Meng et al. 2020). Baroncelli et al. (2016) studied four strains of C. acutatum and illustrated the plasticity of Colletotrichum genomes and showed that major changes in host range are associated with relatively recent changes in gene content. A genome of C. fructicola from apple in China was compared with its reference genome, which identified a number of strong duplication/loss events at key phylogenetic nodes (Liang et al. 2018). Gan et al. (2019) 159 provided the updated genome for C. orbiculare and also provided three draft genomes for C. trifolli, C. sidae and C. spinosum. Colletotrichum higginsianum has a compartmentalized genome consisting of gene-sparse, transposable elements dense regions with more effector candidate genes and genedense, TE-sparse regions harbouring conserved genes which help the pathogen to generate genomic diversity (Tsushima et al. 2019). Comparative genome analysis indicated that there is a rapid evolution of pathogenicity genes in C. tanaceti (Lelwala et al. 2019). Species of Colletotrichum can be used as biocontrol agents and as biocatalysts (C. dematium, C. gloeosporioides, C. graminicola, C. lindemuthianum, C. orbiculare, C.theobromicola, C. trifoli (Jayawardena et al. 2016b)). Jayawardena et al. (2016b) discussed the importance of secondary metabolites produced by species with relation to pathogenesis, medicines, disease control and toxins. Classification—Ascomycota, Pezizomycotina Sordariomycetes, Hypocreomycetidae, Glomerellales, Glomerellaceae Type species—Colletotrichum lineola Corda, in Sturm, Deutschl. Fl., 3 Abt. (Pilze Deutschl.) 3(12): 41 (1831) Distribution—Worldwide Disease symptoms—Anthracnose disease, red rot, crown and stem rots, ripe rot, seedling blights and brown blotch. Anthracnose disease symptoms include defined, often sunken necrotic spots on leaves, stems, flowers or fruits and may show a lot of variation depending on the host (35a−e). Hosts—Pathogens on many host families including, Amaryllidaceae, Amaranthaceae, Anacardiaceae, Annonaceae, Apiaceae, Apocynaceae, Araceae, Araliaceae, Arecaceae, Asparagaceae, Asteraceae, Bignoniaceae, Campanulaceae, Caricaceae, Crassulaceae, Cucurbitaceae, Euphorbiaceae, Fabaceae, Iridaceae, Lamiaceae, Lauraceae, Malvaceae, Melastomataceae, Menispermaceae, Moraceae, Myrtaceae, Oleaceae, Olivaceae, Orchidaceae, Passifloraceae, Pinaceae, Piperaceae, Plumbaginaceae, Poaceae, Podocarpaceae, Polemoniaceae, Proteaceae, Ranunculaceae, Rosaceae, Rubiaceae, Rutaceae, Solanaceae, Theaceae and Vitaceae. Pathogen biology, disease cycle and epidemiology For Colletotrichum biology, disease cycle and epidemiology see Cannon et al. (2012) and De Silva et al. (2017). Morphological based identification and diversity Due to the overlapping morphological characters, species delimitation based on morphology alone is hardly possible (Jayawardena et al. 2016b; Marin-Felix et al. 2017; Fig. 35f–l). Molecular based identification and diversity Cai et al. (2009) proposed the use of a polyphasic approach with multi-loci sequence analyses combined with 13 160 Table 21 DNA barcodes available for Cladosporium 13 Fungal Diversity (2020) 103:87–218 Species Isolate ITS tef1 act Cladosporium acalyphae C. aciculare C. aerium C. aggregatocicatricatum# C. alboflavescens C. allicinum C. allii C. angulosum C. angustiherbarum C. angustisporum C. angustiterminale C. antarcticum C. anthropophilum C. aphidis C. arthropodii C. asperulatum# C. australiense C. austroafricanum C. austrohemisphaericum C. basiinflatum# C. chalastosporoides C. chasmanthicola C. chubutense C. cladosporioides# C. colocasiae# C. colombiae C. coloradense C. crousii C. cucumerinum# C. cycadicola C. delicatulum C. domesticum C. dominicanum C. echinulatum# C. endophyticum C. entadae C. europaeum C. exasperatum C. exile C. fildesense C. flabelliforme C. flavovirens C. floccosum# C. funiculosum C. fusiforme C. gamsianum C. globisporum# C. grevilleae C. halotolerans C. hebeiense# C. herbaroides# CBS 125982* CBS 140488* CBS 143356* CBS 140493* CBS 140690* CBS 121624* CBS 101.81 CBS 140692* CBS 140479* CBS 125983* CBS 140480* CBS 690.92* CBS 140685* CBS 132182* CBS 124043* CBS 126340* CBS 125984* CBS 140481* CBS 140482* CBS 822.84* CBS 125985* CBS 142612* CBS 124457* CBS 112388* CBS 386.64* CBS 274.80B* CBS 143357* CBS 140686* CBS 171.52* CBS 137970* CBS 126344* CBS 143358* CBS 119415* CBS 123191 MFLUCC 17-0599* MFLUCC 17-0919* CBS 134914* CBS 125986* CBS 125987* ChFC-554* CBS 126345* CBS 140462* CBS 140463* CBS 122129* CBS 119414* CBS 125989* CBS 812.96* CBS 114271* CBS 119416* JZB390001* CBS 121626* HM147994 KT600411 MF472897 KT600448 LN834420 EF679350 JN906977 LN834425 KT600378 HM147995 KT600379 EF679334 LN834437 JN906978 JN906979 HM147998 HM147999 KT600381 KT600382 HM148000 HM148001 KY646221 FJ936158 HM148003 HM148067 FJ936159 MF472945 LN834431 HM148072 KJ869122 HM148081 MF472955 DQ780353 JN906980 MG646956 MK347728 HM148056 HM148090 HM148091 JX845290 HM148092 LN834440 LN834416 HM148094 DQ780388 HM148095 HM148096 JF770450 DQ780364 MG516597 EF679357 HM148235 KT600509 MF473324 KT600547 LN834516 EF679425 JN906983 LN834521 KT600475 HM148236 KT600476 EF679405 LN834533 JN906984 JN906985 HM148239 HM148240 KT600478 KT600479 HM148241 HM148242 KY646227 FJ936161 HM148244 HM148310 FJ936163 MF473372 LN834527 HM148316 KJ869236 HM148325 MF473382 JN906986 JN906987 MG646988 HM148481 KT600607 MF473747 KT600645 LN834604 EF679502 JN906996 LN834609 KT600574 HM148482 KT600575 EF679484 LN834621 JN906997 JN906998 HM148485 HM148486 KT600577 KT600578 HM148487 HM148488 KY646224 FJ936165 HM148490 HM148555 FJ936166 MF473795 LN834615 HM148561 KJ869227 HM148570 MF473805 EF101368 JN906999 HM148298 HM148334 HM148335 MN233633 HM148336 LN834536 LN834512 HM148338 JN906988 HM148339 HM148340 JF770472 JN906989 MG516595 EF679432 HM148543 HM148579 HM148580 MN233632 HM148581 LN834624 LN834600 HM148583 EF101372 HM148584 HM148585 JF770473 EF101397 MG516593 EF679509 Fungal Diversity (2020) 103:87–218 Table 21 (continued) 161 Species # C. herbarum C. hillianum C. inversicolor C. ipereniae C. iranicum# C. iridis# C. kenpeggii# C. langeronii C. lebrasiae C. licheniphilum C. limoniforme# C. longicatenatum C. longissimum C. lycoperdinum C. macrocarpum# C. magnoliigena C. michoacanense C. montecillanum C. myrtacearum C. needhamense C. neerlandicum C. neolangeronii C. neopsychrotolerans C. omanense C. ossifragi C. oxysporum# C. paracladosporioides C. parahalotolerans C. paralimoniforme C. parapenidielloides C. parasubtilissimum C. passiflorae# C. passifloricola C. penidielloides C. perangustum# C. phaenocomae C. phlei# C. phyllactiniicola C. phyllophilum C. pini-ponderosae C. prolongatum C. pseudiridis C. pseudochalastosporoides C. pseudocladosporioides# C. psychrotolerans C. pulvericola C. puyae C. ramotenellum# C. rectoides C. rhusicola C. ruguloflabelliforme Isolate ITS tef1 act CBS 121621* CBS 125988* CBS 401.80* CBS 140483* CBS 126346* CBS 138.40* CBS 142613* CBS 189.54* CBS 138283* CBS 125990* CBS 140484* CBS 140485* CBS 300.96* CBS 126347 CBS 121623* MFLUCC 18-1559* CBS 143588* CBS 140486* CBS 126350* CBS 143359* CBS 143360* CBS 797.97* CGMCC 3.18031* SQUCC 13165* CBS 842.91* CBS 125991 CBS 171.54* CBS 139585* CGMCC 3.18103* CBS 140487* CBS 143361* COAD 2135* COAD 2140* CBS 140489* CBS 125996* CBS 128769* CBS 358.69* CBS 126352* CBS 125992* CBS 124456* CGMCC 3.18036* CBS 116463* CBS 140490* CBS 125993* CBS 119412* CBS 143362* CBS 274.80A* CBS 121628* CBS 125994* CBS 140492* CBS 140494* EF679363 HM148097 HM148101 KT600394 HM148110 EF679370 KY646222 DQ780379 KJ596568 HM148111 KT600397 KT600403 DQ780352 HM148112 EF679375 MK347813 LT907958 KT600406 HM148117 MF473142 KP701887 MF473143 KX938383 MH725789 EF679381 HM148118 HM148120 KP701955 KX938392 KT600410 MF473170 MH682175 EF679440 HM148341 HM148345 KT600491 HM148354 EF679447 KY646228 JN906990 KJ596583 HM148355 KT600494 KT600500 EU570259 HM148356 EF679453 MK340864 LT907945 KT600504 HM148361 MF473570 KP701764 EF679516 HM148586 HM148590 KT600589 HM148599 EF679523 KY646225 EF101357 KJ596631 HM148600 KT600592 KT600598 EF101385 HM148601 EF679529 KT600412 HM148121 JF499837 JN906981 HM148150 HM148154 FJ936160 KX938394 EF679383 KT600415 HM148158 DQ780386 MF473226 KT600418 EF679384 HM148193 KT600440 KT600458 KX938400 MH716047 EF679459 HM148362 HM148364 KP701832 KX938409 KT600508 MF473593 MH724943 MH724948 KT600510 HM148365 JF499875 JN906991 HM148394 HM148398 FJ936164 KX938411 EF679461 KT600513 HM148402 JN906992 MF473648 KT600516 EF679462 HM148438 KT600539 KT600557 LT907961 KT600602 HM148606 MF473991 KP702010 MF473992 KX938366 MH716046 EF679535 HM148607 HM148609 KP702077 KX938375 KT600606 MF474018 MH729795 MH729800 KT600608 HM148610 JF499881 JN907000 HM148639 HM148643 FJ936167 KX938377 EF679537 KT600611 HM148647 EF101365 MF474075 KT600614 EF679538 HM148683 KT600637 KT600655 13 162 Table 21 (continued) Fungal Diversity (2020) 103:87–218 Species Isolate ITS tef1 act C. rugulovarians C. salinae C. scabrellum C. silenes C. sinense C. sinuatum C. sinuosum C. sloanii C. soldanellae C. sphaerospermum# C. spinulosum C. subcinereum C. subinflatum C. subtilissimum# C. subuliforme# C. succulentum C. tenellum# C. tenuissimum# C. tianshanense C. tuberosum C. uredinicola C. uwebraunianum C. variabile# C. varians C. velox C. verrucocladosporioides C. verruculosum C. versiforme C. vicinum C. vignae# C. welwitschiicola C. westerdijkiae C. wyomingense C. xanthochromaticum C. xylophilum Toxicocladosporium banksiae CBS 140495* CBS 119413* CBS 126358* CBS 109082* CBS 143363* CGMCC 3.18096* CBS 121629* CBS 143364* CBS 132186* CBS 193.54* CBS 119907* CBS 140465* CBS 121630* CBS 113754* CBS 126500* CBS 140466* CBS 121634* CBS 125995* CGMCC 3.18033* CBS 140693* ATCC 46649 CBS 143365* CBS 121635* CBS 126362* CBS 119417* CBS 126363* CGMCC 3.18099* CBS 140491* CBS 143366* CBS 121.25 CBS 142614* CBS 113746* CBS 143367* CBS 140691* CBS 125997* CBS 128215* KT600459 DQ780374 HM148195 EF679354 MF473252 KX938385 EF679386 MF473253 JN906982 DQ780343 EF679388 LN834433 EF679389 EF679397 HM148196 LN834434 EF679401 HM148197 KX938381 LN834417 AY251071 MF473306 EF679402 HM148224 DQ780361 HM148226 KX938388 KT600417 MF473311 HM148227 KY646223 HM148061 MF473315 LN834415 HM148230 HQ599598 KT600558 JN906993 HM148440 EF679429 MF473675 KX938402 EF679464 MF473676 JN906994 EU570261 EF679466 LN834529 EF679467 EF679475 HM148441 LN834530 EF679479 HM148442 KT600656 EF101390 HM148685 EF679506 MF474102 KX938368 EF679540 MF474103 JN907001 EF101380 EF679542 LN834617 EF679543 EF679551 HM148686 LN834618 EF679555 HM148687 KX938364 LN834601 HM148712 MF474156 EF679556 HM148715 EF101388 HM148717 KX938371 KT600613 MF474161 HM148718 KY646226 HM148548 MF474165 LN834599 HM148721 LT821371 LN834513 HM148467 MF473729 EF679480 HM148470 JN906995 HM148472 KX938405 KT600515 MF473734 HM148473 KY646229 HM148303 MF473738 LN834511 HM148476 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # geographical, ecological and morphological data for reliable species delimitation. Application of this polyphasic approach resulted in the delimitation of almost 200 species, most of them belonging to species complexes such as acutatum, boninense and gloeosporioides. There is no universal set of loci to use when identifying Colletotrichum species. Cannon et al. (2012), Damm et al. (2012a, b, 2013, 2014, 2019, Liu et al. 2016) used ITS, gapdh, chs, act, his and tub2 (with some also gs or cal) for studying species within the acutatum, boninense, dematium, destructivum, gigasporum, orbiculare, spaethianum and truncatum species complexes, while Weir et al. (2012) additionally applied gs, cal and sod2 13 within the gloeosporioides species complex. Hyde et al. (2014), Jayawardena et al. (2016b), Marin-Felix et al. (2017) used ITS, gapdh, chs, act and tub2 to differentiate the species. Using five loci for the whole genus gave similar results to 6-7 loci used for the whole genus. In contrast, Crouch et al. (2009b) applied ITS, sod2, apn2 and mat1/apn2, to study the graminicola and caudatum species complexes. Use of ApMat locus to delimit the species within gloeosporioides species complex was emphasized by Silva et al. (2012) and Sharma et al. (2015) as it provides a higher resolution when compared to previously used loci. However, studies by Liu et al. (2015, 2016) revealed that using this locus with other Fungal Diversity (2020) 103:87–218 Fig. 34 Phylogram generated from Maximum Likelihood analysis based on ITS, tef1 and act sequenced data. Bootstrap support values ≥ 75% and Bayesian posterior probabilities ≥ 0.95 are given near the 163 nodes. The ex-type (ex-epitype) and voucher strains are in bold. The tree is rooted with Toxicocladosporium banksiae CBS 128215 13 164 Fig. 34 (continued) 13 Fungal Diversity (2020) 103:87–218 Fungal Diversity (2020) 103:87–218 loci would provide a satisfactory species delimitation within the gloeosporioides species complex. For species delimitation, application of the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) has proven to be a powerful tool (Cai et al. 2009). Coalescent-based species delimitation methods can also be used to infer the dynamic of divergence, evolutionary process and the relationships among species (McCormack et al. 2009, Liu et al. 2016). Jayawardena et al. (2016b) provided the accepted species for the genus with backbone trees for each species complex and with notes for each accepted species. De Silva et al. (2017) reviewed the lifestyles and how this can be applied to plant biosecurity. Ariyawansa et al. (2015), Yan et al. (2015), Li et al. (2016), De Silva et al. (2017), Hyde et al. (2020a, b), Marin-Felix et al. (2017), Tibpromma et al. (2017, 2018), Samarakoon et al. (2018), Bhunjun et al. (2019) have introduced new species based on morphology, phylogeny and GCPSR evidence. Damm et al. (2019) introduced three new species complexes namely, dracaenophilum, magnum and orchidearum based on morphology and phylogeny. Cabral et al. (2020) based on pathological, morphological, cytogenomic, biochemical and molecular data, assigned the previously known C. kahawae subsp. ciggario as a new species, C. ciggario. At present, based on multi-loci phylogeny there are 14 species complexes. With 59 new species having been added since the last treatment (Marin-Felix et al. 2017), here we present an analysis using five loci (Table 21) for all Colletotrichum species (Fig. 36). From the studies conducted on this genus, it is clear that the resolution of species differs depending on both locus and species. Therefore, to select a better genetic marker and the best secondary barcoding gene/genes is still an ongoing process. Recommended genetic marker (genus level)—ITS Recommended genetic markers (species level)—act, apmat, apn2, cal, chs-1, gapdh, gs, his, mat1/apn2, sod2, and tub2. Accepted number of species—There are 903 epithets listed in Index Fungorum (2020), however, 247 species with molecular data are treated as accepted (Table 22). References—Cai et al. (2009) (polyphasic approach); Hyde et al. (2009a, b) (morphology and accepted species); Cannon et al. (2012) (A review and an updated account of the genus); Crouch et al. (2009a, b, c, 2014), Damm et al. (2009, 2012a, b, 2013, 2014, 2019), Weir et al. (2012) (morphology and phylogeny); Hyde et al. (2014), Jayawardena et al. (2016b), Marin-Felix et al. (2017) (accepted number of species). 97. Mucor Fresen., Beitr. Mykol. 1: 7 (1850) Background Mucor belongs to the order Mucorales, which is among one of the most studied groups of early diverging lineages of fungi. The genus has the largest number of species within the order and half of the sequences submitted to GenBank for Mucorales are of Mucor (Hoffmann et al. 2013; Spatafora et al. 2016; Hyde et al. 2014; Nguyen and Lee 2018). 165 Mucor belongs to the phylum Mucoromycota, subphylum Mucoromycotina, class Mucoromycetes, order Mucorales and family Mucoraceae (Wijayawardene et al. 2018, 2020). It was described by Fresenius in 1850 and the type species is Mucor mucedo. Recent molecular studies of mucoralean species have indicated that Mucor is polyphyletic (Nguyen et al. 2017). However, even with definite results showing the polyphyly of Mucor, few clear lineages within Mucor are recognized. Some of these lineages share innate characteristics, such as sporangium size and branching of tall sporangiophores and the morphology is still widely used in current taxonomy (Walther et al. 2013). Analysis of internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequence data of several mucoralean species, showed that some Mucor species with curved sporangiophores grouped with species of Backusella and hence was transferred to Backusella (Walther et al. 2013; Nguyen et al. 2017). Mucor species are commonly isolated from soil, dung, insect, and fruits (Benny 2008). Some species are of biotechnological importance such as biofuel, enzyme, terpernoid production and biotransformation while other species cause mucoromycosis in immunosuppressed humans (Nguyen et al. 2017; Steve et al. 2018; Morin-Sardin et al. 2017). Comparative analyses of five Mucor species based on their lifestyles (M. fuscus and M. lanceolatus (used for cheese production), M. circinelloides and M. racemosus (opportunistic pathogens) and M. endophyticus (an endophyte)) revealed the core transcriptome comprising 5566 orthogroups included genes potentially involved in secondary metabolism. Due to the wide taxonomic range investigated, the five transcriptomes also displayed specificities that can be linked to the different lifestyles, such as differences in the composition of transcripts identified as virulence factors or carbohydrate transporters. Research on this genus has changed its course to identify the link between genetic and biological data, especially in terms of lifestyle and adaptations to a given habitat (Lebreton et al. 2019) (Figs. 37, 38). Classification—Zygomycota, Mucoromycotina, Mucoromycetes, Mucorales, Mucorineae, Mucoraceae Type species—Mucor mucedo Fresen. Distribution—Worldwide Disease symptoms—Mucor rot and soft rot Mucor species especially M. fragilis, M. irregularis, M. piriformis and M. racemosus often cause postharvest diseases such as Mucor rot and soft rot. The initial symptoms of Mucor rot are similar to plant diseases caused by green mold, blue mold, and sour mold. The infected tissue becomes soft and watery. The lesions turn light to dark brown and as the infection progresses, white or shiny grey sporangiophores form at the lesions. Fungal growth spreads across the whole host and masses of sporangiophores bearing black to pale brown sporangia are observed. Decaying fruits become “juicy” within which are abundant spores of 13 166 Fungal Diversity (2020) 103:87–218 the fungus (Li et al. 2014; Saito et al. 2016). Ito et al. (1979) found that three species of fruit flies namely Certitis capitata, Dacus cucurbitae and D. dorsalis, can transmit Mucor rot in guava. Soft rot caused by Mucor racemosus results in watersoaked appearance followed by a softening of the infected part. When the disease progresses growth of white mycelium and brownish to grey sporangia can be observed. Finally, the infected tissue is broken down and disintegrates in a watery rot (Kwon and Hong 2005; López et al. 2016). Fig. 36 Phylogram generated from MP analysis based on combined ▸ sequences of ITS, gapdh, chs, act and tub2 sequences of all species of Colletotrichum with molecular data. Related sequences were obtained from GenBank. Two hundred and fourty nine taxa are included in the analyses, which comprise 2296 characters including gaps, of which 868 characters are constant, 295 characters are parsimony-uninformative and 1133 characters parsimony-informative. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 10088 steps (CI = 0.283, RI=0.840, RC = 0.237, HI = 0.717) in the third tree. Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted with Monilochaetes infuscans (CBS 869.96) and M. populi (CBS 139623). MP bootstrap support value ≥ 50% and BYPP ≥ 0.9 are shown respectively near the nodes. Ex-type strains are in bold Fig. 35 Colletotrichum sp. a Chilli anthracnose symptoms b Crown rot of strawberry c Leaf blight of Cannas sp. d, e strawberry anthracnose symptoms f, g Conidiomata and spore mass h Conidiophore i Setae j Conidiogenous cells and curved conidia k Conidia of C. gloeosporioides l Appressoria. Phylogram generated from RAxML analysis based on combined sequences of ITS and LSU of Mucorand Backusella species. Eighty-one taxa were used for the analysis, which consisted 1256 characters includinggaps. The tree is rooted using Backusella lamprospora (CBS 195.28), and B. grandis (CBS 186.87). Likelihoodof the best scoring ML tree was -16174.718247. The concatenated matrix contained 657 distinct alignmentpatterns with 22.27% of undetermined characters or gaps. Estimated base frequencies were as follows; A =0.302146, C = 0.168433, G = 0.219872, T = 0.309549; substitution rates AC = 0.776817, AG = 3.154911, AT =1.674079, CG = 0.632500, CT = 4.808262, GT = 1.000000; gamma distribution shape parameter α = 0.291909.Type species in the dataset are indicated using T. Maximum likelihood RAxML bootstrap support value ≥ 70%and Bayesian posterior probabilities ≥ 0.70 are shown near the nodes (ML/BYPP). – indicates bootstrap supportvalues lower than 70% and * shows unrecovered branching 13 Fungal Diversity (2020) 103:87–218 167 13 168 Fungal Diversity (2020) 103:87–218 Fig. 36 (continued) Hosts—Wide host range including, Actinidia deliciosa, Citrus reticulata, Dioscorea species, Fragaria × ananassa, Mangifera indica, Manihot esculenta, Prunus species, Psidium guajava, Solanum melongena, Solanum lycopersicum and Vitis species (Farr and Rossman 2020). 13 Pathogen biology, disease cycle and epidemiology The pathogen reproduces asexually. Mucor rot often develops by infecting punctured wounds and cracks on the surface of the fruit, stem end or calyx of the host. In the early stages of the infection, the fruit becomes soft and Fungal Diversity (2020) 103:87–218 169 Table 22 DNA barcodes available for Colletotrichum, isolates used in the phylogenetic analyses Species name Isolate no ITS gapdh chs-1 act tub2 Complex Colletotrichum abscissum# C. acerbum C. acidae C. acutatum# C. aenigma# C. aericola# C. aeschynomenes# C. agaves C. alcornii C. alatae# C. alienum# C. americae-borealis# C. annellatum C. anthrisci C. antirrhinicola C. aotearoa C. araceaerum C. arboricola# C. artocarpicola# C. arxii C. asianum# C. atractylodicola C. australe C. axonopodi C. beeveri C. baltimorense C.bidentis C. bletillum C. boninense# C. brasiliense C. brassicicola C. brevisporum# C. brisbaniense C. bryoniicola C. cacao# C. cairnsense# C. camelliae# C. camelliae-japonicae C. carthami# C. catinaense# C. cattleyicola C. cariniferi C. caudatum C. caudasporum C. cereale# C. changpingense# C. chlorophyti# C. chiangraiense C. chrysanthemi# C. chrysophillum COAD 1877* CBS 128530* MFLUCC 17-2659* CBS 112996* ICMP 18608* CGMCC 3.19667* ICMP 17673 CBS 118190* IMI176619* CBS 304.67* ICMP 12071* CBS 136232* CBS 129826* CBS 125334* CBS 102189* ICMP 18537* CGMCC 3.14982* CBS 144795* MFLUCC 18-1167* CBS 132511* ICMP 18580* CGMCC 3.18761* CBS 116478* IMI 279189/279189AA CBS 128527* BPI892771* COAD 1020* CGMCC 3.15117* CBS 123755* CBS 128501* CBS 101059* BCC 38876* CBS 292.67* CBS 109849* CBS 119297* BRIP 63642* CGMCC3.14925* CGMCC3.18118* SAPA100011* CBS 142417* CBS 170.49* MFLUCC 14-0100* CBS 131602* CGMCC 3.15106* CBS 129663* MFLUCC 15-0022* IMI 103806* MFLUCC 14-0119* IMI 364540* URM7368* KP843126 JQ948459 MG996505 JQ005776 JX010244 MK914635 JX010176 DQ286221 JX076858 JX010190 JX010251 KM105224 JQ005222 GU227845 KM105180 JX010205 KX853166 MH817944 MN415991 KF687716 JX010196 KR149280 JQ948455 EU554086 JQ005171 JX076866 KF178481 JX625178 JQ005153 JQ005235 JQ005172 JN050238 JQ948291 KM105181 MG600772 KU923672 KJ955081 KX853165 AB696998 KY856400 MG600758 MF448521 JX076860 JX625162 JQ005774 KP683152 GU227894 MF448522 JQ948273 KX094252 KP843129 JQ948790 MH003691 JQ948677 JX010044 MK935455 JX009930 KP843132 JQ949120 MH003694 JQ005797 JX009774 MK935541 JX009799 KP843141 JQ949780 MH003697 JQ005839 JX009443 MK935374 JX009483 KP843135 JQ950110 MH003700 JQ005860 JX010389 MK935498 JX010392 JX009990 JX010028 KM105579 JQ005309 GU228237 KM105531 JX010005 KX893585 MH817950 MN435568 KF687843 JX010053 KR259334 JQ948786 JX009837 JX009882 KM105294 JQ005396 GU228335 KM105250 JX009853 JX009471 JX009572 KM105434 JQ005570 GU227943 KM105390 JX009854 KX893577 MH817956 MN435569 MN435570 KF687780 KF687802 JX009867 JX009584 KR259333 KR132243 JQ949116 JQ949776 JX010383 JX010411 KM105504 JQ005656 GU228139 KM105460 JX010420 KX893581 MH817962 MN435567 KF687881 JX010406 KU058178 JQ950106 JQ005258 JQ005345 JQ005605 KF178506 KC843506 JQ005240 JQ005322 JQ005259 JN050227 JQ948621 KM105532 MG600832 KU923704 KJ954782 KX893584 KF178530 acutatum acutatum truncatum acutatum gloeosporioides gloeosporioides gloeosporioides singleton caudatum gloeosporioides gloeosporioides destructivum boninense dematium destructivum gloeosporioides singleton acutatum gloeosporioides gigasporum gloeosporioides destructivum acutatum singleton boninense caudatum orbiculare spaethianum boninense boninense boninense magnum acutatum destructivum magnum acutatum gloeosporioides boninense acutatum boninense orchidearum singleton caudatum caudatum graminicola gloeosporioides singleton gigapsorum acutatum gloeosporioides JQ005519 KF178602 JX625207 JQ005588 JQ005669 JQ005606 JN050244 JQ949942 KM105461 MG601039 KU923688 KJ955230 KX893580 AB696992 KY856224 KY856136 KY855971 KY856482 MG600819 MG600866 MG600963 MG601025 MH351274 KC843512 KF178578 KC843542 JQ005327 JQ005501 JQ005409 JQ005583 JQ005346 JQ005520 JN050216 JQ948952 JQ949612 KM105251 KM105391 MG600878 MG600976 KU923710 KU923716 KJ954363 KX893576 KC843526 JQ005795 JQ005837 KP852469 KP852449 KP683093 GU228286 GU228384 GU227992 MH376383 JQ948603 JQ948934 JQ949594 KX094183 KX094083 KX093982 JX625190 JQ005858 KP852490 GU228188 MH351275 JQ949924 KX094285 13 170 Fungal Diversity (2020) 103:87–218 Table 22 (continued) Species name # C. ciggaro C. circinans C. citri C. citricola# C. clidemiae C. cliviicola# C. cobbittiense C. coccodes# C. coelogynes C. colombiense C. condaoense C. conoides# C. constrictum C. cordylinicola# C. cosmi C. costaricense C. curcumae# C. cuscutae C. cymbidiicola# C. dacrycarpi C. dematium# C. destructivum# C. doitungense C. dracaenophilum# C. duyunensis C. echinochloae C. eleusines C. endophytica# C. endophytum C. eremochloae# C. eriobotryae# C. eryngiicola C. excelsum-altitudinum C. euphorbiae C. falcatum# C. feijoicola C. fioriniae# C. fructi C. fructicola# C. fructivorum# C. fuscum# C. fusiforme C. gigasporum# C. gloeosporioides# C. godetiae# C. graminicola# C. grevilleae C. grossum# C. guajavae C. guizhouensis 13 Isolate no ITS gapdh chs-1 act tub2 Complex ICMP 18539* CBS 221.81 CBS 134233* CBS 134228* ICMP 18658* CBS 125375* BRIP 66219a* CBS 369.75* CBS 132504* CBS 129818* CBS 134299* CAUG17* CBS 128504* MFU 09-0551* CBS 853.73* CBS 330.75* IMI 288937* IMI 304802* IMI 347923* CBS 130241* CBS 125.25* CBS 136228* MFLUCC 14-0128* CBS 118199* CGMCC 3.15105* MAFF 511473* MAFF 511155* MFLUCC 13–0418* CGMCC 3.15108 * CBS 129661* GLMC 1935* MFLUCC 17-0318* CGMCC 3.15130* CBS 134725* CBS 147945* CBS 144633 * CBS 128517* CBS 346.37* ICMP 18581* CBS 133125* CBS 133701* MFLU 13-0291* CBS 133266* CBS 112999* CBS 133.44* M 1.001* CBS 132879* CAUG7* IMI 350839* CGMCC 3.15112* JX010230 GU227855 KC293581 KC293576 JX010265 MG600733 MH087016 HM171679 MG600713 JQ005174 MH229914 KP890168 JQ005238 JX010226 JQ948274 JQ948180 GU227893 JQ948195 JQ005166 JQ005236 GU227819 KM105207 MF448524 JX519222 JX625160 AB439811 JX519218 KC633854 JX625177 JX519220 MF772487 KY792726 HM751815 KF777146 JQ005772 MK876413 JQ948292 GU227844 JX010165 JX145145 KM105174 KT290266 KF687715 JQ005152 JQ948402 JQ005767 KC297078 KP890165 JQ948270 JX625158 JX009966 GU228247 KC293741 KC293736 JX009989 MG600795 MH094133 HM171673 MG600776 JQ005261 MH229920 KP890162 JQ005325 JX009975 JQ948604 JQ948510 GU228285 JQ948525 JQ005253 JQ005323 GU228211 KM105561 MH049480 JX546707 KC843515 JX009800 GU228345 KY856138 KC293792 JX009877 MG600850 MH094135 JQ005796 MG600836 JQ005348 MH229926 KP890156 JQ005412 JX009864 JQ948935 JQ948841 GU228383 JQ948856 JQ005340 JQ005410 GU228309 KM105277 JX009523 GU227953 KY855973 KC293616 JX009537 MG600939 MH094134 HM171667 MG600920 JQ005522 JX010434 GU228149 KC293661 KC293656 JX010438 MG601000 MH094137 JQ005859 MG600980 JQ005608 MH229923 KP890174 JQ005672 JX010440 JQ949925 JQ949831 GU228187 JQ949846 JQ005600 JQ005670 GU228113 KM105487 MH351277 JX519247 JX625187 gloeosporioides dematium acutatum boninense gloeosporioides orchidearum gloeosporioides singleton dracaenophilum boninense boninense gloeosporioides boninense gloeosporioides acutatum acutatum truncatum acutatum boninense boninense dematium destructivum boninense dracaenophilum caudatum graminicola graminicola gloeosporioides graminicola graminicola acutatum dematium dracaenophilum singleton graminicola boninense acutatum dematium gloeosporioides gloeosporioides destructivum truncatum gigasporum gloeosporioides acutatum graminicola gloeosporioides gloeosporioides acutatum spaethianum JX519230 JX519226 KP890144 JQ005586 HM470234 JQ949595 JQ949501 GU227991 JQ949516 JQ005514 JQ005584 GU227917 KM105417 MH376385 JX519238 KC843530 JX519234 KF306258 KC843533 JX519228 JX519236 MF795423 MN191653 MN191648 KY792723 KY792720 KY792717 KC843502 KC843548 KF777131 KF777128 KF777125 JQ005793 JQ005835 MK876475 MK876466 JQ948622 JQ948953 JQ949613 GU228236 GU228334 GU227942 JX010033 JX009866 FJ907426 KC832854 KC843521 JX519243 JX625206 JX519245 MF795428 KY792729 JX625211 KF777247 JQ005856 MK876507 JQ949943 GU228138 JX010405 JX145196 KM105524 KM105244 KM105384 KM105454 KT290255 KT290253 KT290251 KT290256 KF687822 KF687761 KF687866 JQ005239 JQ005326 JQ005500 JQ005587 JQ948733 JQ949063 JQ949723 JQ950053 JQ005788 JQ005830 JQ005851 KC297010 KC296987 KC296941 KC297102 KP890159 KP890153 KP890141 KP890171 JQ948600 JQ948931 JQ949591 JQ949921 KC843507 KC843536 JX625185 Fungal Diversity (2020) 103:87–218 171 Table 22 (continued) Species name Isolate no ITS C. hanaui C. hebeiense# C. hedericola C. helleniense# C. henanense# C. hemerocallidis C. higginsianum# C. hippeastri C. horii# C. hystricis# C. hsienjenchang C. incanum C. indonesiense C. insertae C. jacksonii C. jasminigenum C. javanense# C. jiangxiense C. jinshuiense# C. jishouense C. johnstonii C. kahawae# C. kakivorum# C. karstii# C. kinghornii C. laticiphilum# C. lauri C. ledebouriae C. lentis# C. liaoningense# C. lilii C. lini C. limetticola C. limonicola# C. lindemuthianum# C. lineola# C. liriopes# C. lobatum C. lupini# C. magnisporum C. makassarense# C. magnum C. malvarum C. melonis# C. menispermi C. metake C. merremiae C. miscanthi C. musae# C. musicola# MAFF 305404* MFLUCC13–0726* MFLU 15-0689* CBS 142418* CGMCC 3.17354* CDLG5 IMI 349061* CBS 125376* NBRC 7478* CBS 142411* MAFF 243051 ATCC 64682* CBS 127551* MFLU 15-1895* MAFF 305460* CGMCC LLTX-01* CBS 144963a* CGMCC 3.17363* CGMCC 3.18903* GMBC0209* CBS 128532* IMI 319418* KCTC 46679* CORCG6* CBS 198.35* CBS 112989* MFLUCC 17-0205* CBS 141284* CBS 127604* CGMCC 3.17616* CBS 109214/BBA 62147* CBS 172.51* CBS 114.14* CBS 142410* CBS 144.31* CBS 125337* CBS 119444* IMI 79736* CBS 109225* CBS 398.84* CBS 143664a* CBS 519.97* CBS 521.97* CBS 159.84* MFLU 14-0625* MAFF 244029 CBS 124955* MAFF 510857* CBS 116870* CBS 132885* JX519217 KF156863 MN631384 KY856446 KJ955109 JQ400005 KM105184 JQ005231 GQ329690 KY856450 AB738855 KC110789 JQ948288 KX618686 JX519216 HM131513 MH846576 KJ955201 MG748077 MH482929 JQ948444 JX010231 LC324781 HM585409 JQ948454 JQ948289 KY514347 KX228254 JQ005766 KP890104 GU227810 JQ005765 JQ948193 KY856472 JQ005779 GU227829 GU227804 MG600768 JQ948155 KF687718 MH728812 MG600769 KF178480 JQ948194 KU242357 AB738859 MG600765 JX519221 HQ596292 MG600736 tub2 Complex JX519225 KF289008 KF377532 MN635794 MN635795 KY856270 KY856186 KY856019 KJ954810 KM023257 JQ400012 Q399998 JQ399991 KM105535 KM105254 KM105394 JQ005318 JQ005405 JQ005579 GQ329681 JX009752 JX009438 KY856274 KY856190 KY856023 AB738846 AB738845 KC110807 KC110825 JQ948618 JQ948949 JQ949609 KX618684 KX618683 KX618682 JX519224 JX519233 HM131499 HM131508 MH846572 MH846573 MH846575 KJ954902 KJ954471 MG747995 MG747913 MG747767 MH681658 MH708135 JQ948775 JQ949105 JQ949765 JX010012 JX009813 JX009452 LC324787 LC324783 LC324785 HM585391 HM582023 HM581995 JQ948785 JQ949115 JQ949775 JQ948619 JQ948950 JQ949610 KY514344 KY514341 KY514338 KX228357 KM105597 JQ005787 JQ005829 KP890135 KP890127 KP890097 GU228202 GU228300 GU227908 KM105581 JQ005786 JQ005828 JQ948523 JQ948854 JQ949514 KY856296 KY856213 KY856045 JX546712 JQ005800 JQ005842 GU228221 GU228319 GU227927 GU228196 GU228294 GU227902 MG600828 MG600874 MG600972 JQ948485 JQ948816 JQ949476 KF687842 KF687782 KF687803 MH728820 MH805850 MH781480 MG600829 MG600875 MG600973 KF178504 KF178529 KF178577 JQ948524 JQ948855 JQ949515 KU242356 KU242355 KU242353 JX519242 KF288975 MG600825 MG600872 JX519229 HQ596299 JX009896 MG600798 MG600853 MG601032 JX519246 HQ596280 MG601003 graminicola gloeosporioides gloeosporioides gloeosporioides gloeosporioides dematium destructivum boninense gloeosporioides gloeosporioides singleton spaethianum acutatum dematium graminicola truncatum acutatum gloeosporioides dematium gigasporum acutatum gloeosporioides dematium boninense acutatum acutatum acutatum singleton destructivum magnum spaethianum destructivum acutatum boninense orbiculare dematium spaethianum magnum acutatum gigasporum gloeosporioides magnum orbiculare acutatum dematium singleton magnum graminicola gloeosporioides orchidearum gapdh chs-1 act KF377495 MG600969 JX519237 HQ596284 MG600942 KY856528 KJ955257 JQ400019 KM105464 JQ005665 JX010450 KY856532 KC110816 JQ949939 KX618685 JX519241 HM153770 MH846574 KJ955348 MG748157 MH727473 JQ950095 JX010444 LC324791 HM585428 JQ950105 JQ949940 KY514350 JQ005850 KP890111 GU228104 JQ005849 JQ949844 KY856554 JQ005863 GU228123 GU228098 MG601035 JQ949806 KF687882 MH846563 MG601036 KF178601 JQ949845 KU242354 13 172 Fungal Diversity (2020) 103:87–218 Table 22 (continued) Species name Isolate no ITS C. navitas C. neosansevieriae C. nicholsonii C. nigrum# C. novae-zelandiae# C. nupharicola# C. nymphaeae# C. ocimi C. ochracea C. okinawense# C. oncidii C. orbiculare# C. orchidearum# C. orchidophilum# C. orchidis C. panacicola C. pandanicola C. panamense C. paranaense# C. parallelophorum C. parsonsiae C. parthenocissicola C. paspali C. paxtonii C. petchii C. perseae# C. phaseolorum# C. phormii C. phyllanthi# C. piperis# C. pisicola C. plurivorum# C. pseudoacutatum# C. pseudomajus C. pseudotheobromicola# C. psidii C. proteae C. pyricola C. pyrifoliae# C. queenslandicum# C. radicis C. rhexiae C. rhombiforme# C. riograndense C. roseum C. rusci C. salicis# C. salsolae# C. sambucicola C. sansevieriae# CBS 125086* CPC 25127* MAFF 511115* CBS 169.49* CBS 128505* CBS 470.96* CBS 515.78* CBS 298.94* CGMCC 3.15104* MAFF 240517* CBS 129828* CBS 570.97* CBS 135131* CBS 632.80* MFLUCC 17-1302* C08087* MFLUCC 17-0571* CBS 125386* CBS 134729* MFLUCC 14-0083* CBS 128525* MFLUCC 17-1098* MAFF 305403* IMI 165753* CBS 378.94* CBS 141365* CBS 157.36 CBS 118194* CBS 175.67* IMI 71397* CBS 724.97* CBS 125474* CBS 436.77* CBS 571.88* MFLUCC 18–1602* CBS 145.29* CBS 132882* CBS 128531* CGMCC 3.18902* ICMP 1778* CBS 529.93* CBS 133134* CBS 129953* ICMP 20083* CBS 145754 * CBS 119206* CBS 607.94* ICMP 19051* MFLUCC 16–1388* MAFF 239721/Sa-1-2 JQ005769 KR476747 JQ005770 JX546838 JQ005228 JX010187 JQ948197 KM105222 JX625156 MG600767 JQ005169 KF178466 MG600738 JQ948151 MK502144 GU935869 MG646967 MG600766 KC204992 MF448525 JQ005233 MK629452 JX519219 JQ948285 JQ005223 KX620308 GU227896 JQ948446 JQ005221 MG600760 KM105172 MG600718 JQ948480 KF687722 MH817395 JX010219 KC297079 JQ948445 MG748078 JX010276 KF687719 JX145128 JQ948457 KM655299 MK903611 GU227818 JQ948460 JX010242 KY098781 LC179806 13 gapdh chs-1 act tub2 Complex JQ005790 JQ005832 KR476790 JQ005833 JX546646 JQ005576 JX009437 JQ949518 KM105432 KC843527 MG600971 JQ005517 KF178563 MG600944 JQ949472 MK496853 GU944758 MG646938 MG600970 KC205077 JQ005853 KR476797 JQ005854 JX546885 JQ005662 JX010398 JQ949848 KM105502 JX625183 MG601034 JQ005603 KF178587 MG601005 JQ949802 MK496859 GU935889 MG646926 MG601033 KC205060 MH351280 JQ005667 MK639360 JX519244 JQ949936 JQ005657 KX620341 GU228190 JQ950097 JQ005655 MG601027 KM105452 MG600985 JQ950131 KF687883 MH853684 JX010443 KC297101 JQ950096 MG748158 JX010414 KF687869 JX145179 JQ950108 KM655300 MK903607 GU228112 JQ950111 JX010403 KY098782 LC180128 graminicola singleton graminicola singleton boninense gloeosporioides acutatum destructivum caudatum magnum boninense orbiculare orchidearum singleton dematium destructivum gloeosporioides magnum acutatum singleton boninense dematium graminicola acutatum boninense gloeosporioides dematium acutatum boninense orchidearum destructivum orchidearum singleton gigasporum gloeosporioides gloeosporioides gloeosporioides acutatum singleton gloeosporioides gigasporum gloeosporioides acutatum spaethianum acutatum singleton acutatum gloeosporioides dematium singleton KR476791 JQ005791 JX546742 JX546693 JQ005315 JQ005402 JX009972 JX009835 JQ948527 JQ948858 KM105577 KM105292 KC843513 MG600827 JQ005256 JQ005343 KF178490 KF178515 MG600800 MG600855 JQ948481 JQ948812 MK496857 MK496855 GU935849 MG646934 MG646931 MG600826 MG600873 KC205026 KC205043 MK165695 JQ005320 JQ005407 MK639362 MK639356 JX519227 JQ948615 JQ948946 JQ005310 JQ005397 KX620242 GU228288 GU228386 JQ948777 JQ949107 JQ005308 JQ005395 MG600820 MG600867 KM105522 KM105242 MG600781 MG600841 JQ948811 JQ949141 KF687826 KF687779 MH853675 MH853678 JX009967 JX009901 KC297009 KC296986 JQ948776 JQ949106 MG747996 MG747914 JX009934 JX009899 KF687825 KF687762 JQ948788 KM655298 MK903603 GU228210 JQ948791 JX009916 KY098780 LC180130 JQ005581 MK639358 JX519235 JQ949606 JQ005571 KX620145 GU227994 JQ949767 JQ005569 MG600964 KM105382 MG600925 JQ949801 KF687801 MH853681 JX009515 KC296940 JQ949766 MG747768 JX009447 KF687785 JQ949118 JQ949778 KM655297 KM655295 MK903604 GU228308 GU227916 JQ949121 JQ949781 JX009863 JX009562 KY098779 KY098778 LC180129 LC180127 Fungal Diversity (2020) 103:87–218 173 Table 22 (continued) Species name # C. scovillei C. sedi C. serranegrense C. shisoi# C. siamense# C. sidae C. simmondsii# C. sloanei C. somersetense C. sonchicola C. sojae C. spaethianum# C. spinaciae# C. spinosum C. sublineola# C. sydowii C. syzygiicola C. tabacum C. tainanense C. tanaceti# C. tamarilloi# C. tebeesti C. theobromicola# C. temperatum C. ti# C. tofieldiae C. tongrenense C. torulosum C. trichellum C. trifolii# C. tropicale# C. tropicicola C. truncatum# C. utrechtense C. verruculosum C. vietnamense C. vignae C. viniferum# C. vittalense C. walleri C. wanningense# C. watphraense C. wuxiense# C. xanthorrhoeae C. yulongense C. yunnanense C. zoysiae Isolate no ITS gapdh act tub2 Complex CBS 126529* MFLUCC14-1002* COAD 2100a* JCM 31818* MFU 090230* CBS 504.97* CBS 122122* IMI 364297* CBS 131599* MFLUCC 17-1299* ATCC 62257* CBS 167.49* CBS 128.57 CBS 515.97* CBS 131301* CBS135819* MFLUCC 10-0624* CPC 18945* CBS 143666a* CBS 132693* CBS 129814* CBS 522.97* ICMP 18649* CBS 133122* ICMP 4832* CBS 495.85* GZU_TRJ1-37/ GMBC0209* CBS 128544* CBS 217.64* CBS 158.83* CBS 124949* BCC 38877* CBS 151.35* CBS 130243* IMI 45525* LD16(L2)* CBS 501.97* GZAAS5.08601* CBS 181.82* CBS 125472* CGMCC 3.18936* MFLUCC 14-0123* CGMCC 3.17894* BRIP 45094* CFCC 50818* CBS 132135* MAFF238573* JQ948267 KM974758 KY400111 MH660930 FJ972613 KF178472 JQ948276 JQ948287 JX076862 KY962757 MG600749 GU227807 GU227847 KF178474 JQ005771 KY263783 KF242094 KM105204 MH728818 JX218228 JQ948184 KF178473 JX010294 JX145159 JX010269 GU227801 MH482933 JQ948597 JQ948928 KM974755 KM974754 KY407894 MH660931 MH660929 FJ972575 JX009865 KF178497 KF178521 JQ948606 JQ948937 JQ948617 JQ948948 JQ949588 KM974756 KY407892 MH660928 FJ907423 KF178569 JQ949597 JQ949608 JQ949918 KM974757 KY407896 MH660932 FJ907438 KF178593 JQ949927 JQ949938 KY962754 MG600810 GU228199 GU228239 KF178498 KY962751 MG600860 GU228297 GU228337 KF178523 JQ005792 KY263785 KY263787 KF242156 KM105557 KM105274 MH728823 MH805845 JX218243 JX259268 JQ948514 JQ948845 KF178505 KF178522 JX010006 JX009869 KY962748 MG600954 GU227905 GU227945 KF178571 JQ005834 KY263791 KF157801 KM105414 MH781475 JX218238 JQ949505 KF178570 JX009444 acutatum dematium gigasporum destructivum gloeosporioides orbiculare acutatum acutatum caudatum dematium orchidearum spaethianum dematium orbiculare graminicola singleton gloeosporioides destructivum gloeosporioides destructivum acutatum orbiculare gloeosporioides gloeosporioides gloeosporioides spaethianum dracaenophilum JQ005164 GU227812 KF178478 JX010264 JN050240 GU227862 KM105201 GU227806 KF687721 KM105183 JN412804 MG600734 JQ948275 MG830462 MF448523 KU251591 JX010261 MH751507 JX546804 JX076871 JQ005251 GU228204 KF178502 JX010007 JN050229 GU228254 KM105554 GU228198 KF687832 KM105534 JN412798 MG600796 JQ948605 MG830318 MH049479 KU252045 JX009927 MK108986 JX546706 JQ005512 GU227910 KF178575 JX009489 JN050218 GU227960 KM105411 GU227904 KF687792 KM105393 JN412795 MG600940 JQ949596 MG830270 MH376384 KU251672 JX009478 MH777394 JX519239 chs-1 MG601016 GU228101 GU228141 KF178595 JQ005855 KY263793 KF254880 KM105484 MH846558 JX218233 JQ949835 KF178594 JX010447 JX145211 JX009952 JX009898 JX009520 JX010442 GU228193 GU228291 GU227899 GU228095 MH705332 MH717074 MH729805 JQ005338 GU228302 KF178527 JX009870 GU228352 KM105271 GU228296 KF687769 KM105253 MG600851 JQ948936 MG830302 KU251939 JX009823 MH793605 JX519231 JQ005598 GU228106 KF178599 JX010407 JN050246 GU228156 KM105481 GU228100 KF687877 KM105463 JN412813 MG601001 JQ949926 MG830286 MH351276 KU252200 JX010448 MK108987 JX519248 boninense singleton orbiculare gloeosporioides dracaenophilum truncatum destructivum spaethianum gigasporum destructivum gloeosporioides orchidearum acutatum acutatum boninense gloeosporioides gloeosporioides gloeosporioides dracaenophilum caudatum Ex-type/ex-epitype/ex-neotype/ex-lectotype strains in bold and marked with an asterisk (*).Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # 13 174 13 Fungal Diversity (2020) 103:87–218 Fungal Diversity (2020) 103:87–218 ◂Fig. 37 Phylogram generated from RAxML analysis based on com- bined sequences of ITS and LSU of Mucor and Backusella species. Eighty-seven taxa were used for the analysis, which consisted of 1264 characters including gaps. The tree is rooted using Backusella lamprospora (CBS 195.28), and B. grandis (CBS 186.87). Likelihood of the best-scoring ML tree was − 17553.567209. The concatenated matrix contained 716 distinct alignment patterns with 21.98% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.302082, C = 0.168706, G = 0.219403, T = 0.309809; substitution rates AC = 0.749467, AG = 2.977575, AT = 1.651634, CG = 0.631954, CT = 4.647089, GT = 1.000000; gamma distribution shape parameter α = 0.302610. The type species are in bold. Scale bar indicates the number of substitutions per site. ML bootstrap support values greater than 70% are shown near the nodes appears water-soaked. The lesions formed are quasicircular or irregular, light to dark brown and the sporangiophores protrude through the wounds (Kwon and Hong 2005; Saito et al. 2016; Michailides and Spotts 1990). As the infection advances, the infected part disintegrates into a watery rot and the infection spreads and extends to all extremities of the fruit or even the surface of the container. The infected part is covered with a large mass of mycelium with erect sporangiophores and sporangia (Saito et al. 2016; Michailides and Spotts 1990). When tested, rotten apple and pear by some Mucor species release an alcoholic odour while Mucor rot in peaches and nectarines caused by M. piriformis emits a pleasant aromatic odour. At an advanced stage, Mucor rot can be distinguished from other rots caused by Rhizopus or Gilbertella. Differences are observed in the mycelial character, growth, sporangiophores and sporangia. For Mucor rot, erect, white or yellowish sporangiophore with grey to black sporangia is observed which covers the decay lesion densely. However, for Rhizopus rot, the mycelia are interwoven with stolons with dark sporangiophores and black sporangia. The sporangial wall eventually dries and falls apart while in Mucor rot, the sporangia absorb water from the sporangial wall which dissolves (Michailides and Spotts 1990). Morphology- based identification and diversity Mucor is characterized by fast-growing colonies. The sporangiophores are simple or branched without basal rhizoids. However, under some conditions, they form rhizoids. These species normally form globose sporangia, containing the columella and spores. The sporangium is non-apophysate with pigmented and ornamented zygosporangial walls. Arthrospores, chlamydospores, and zygospores may be produced by some species. The zygospores lack appendaged suspenders and broad aseptate or sparsely septate hyphae are commonly found in Mucor species (Nguyen et al. 2016). When spores from sporangia are released, a remaining collarette is observed. The sporangiospores are round or slightly elongated (Larone 1995; Sutton et al. 1998; de Hoog et al. 2000). With 76 accepted species, the genus is the largest and most studied group in Mucorales (Walther et al. 2019). 175 Molecular identification and diversity The present taxonomy of Mucor is mostly based on morphological characters and interfertility tests. The genus was previously diagnosed using biological species recognition and morphological species recognition (Schipper 1973; Hermet et al. 2012). However, identification often fails with only morphology hence phylogenetic species recognition has been used to resolve species (Taylor et al. 2000). The use of multi-gene (ITS, tef1 and act) phylogenetic analysis showed that Mucor is not monophyletic (Nguyen et al. 2017). An extensive study by Walther et al. (2013), using about 400 Mucor strains, led to a refinement in the classification of Mucor species. Phylogeny-based on 28S rDNA led to the transfer of some species to different groups and it was shown that some of these groups intermingled with other genera, such as Chaetocladium and Helicostylum, which do not belong to Mucoraceae. The use of five markers (ITS, rpb1, tsr1, mcm7 and cfs) phylogeny by Wagner et al. (2019), combined with phenotypic studies, mating tests and the determination of the maximum growth temperatures revealed 16 phylogenetic species of which 14 showed distinct phenotypical traits and were recognized as discrete species. Recommended genetic markers (genus level)—LSU and SSU Recommended genetic markers (species level)—ITS and rpb 1 Accepted number of species—There are 735 species epithets in Index Fungorum (2020), however only 76 species have DNA sequence data (Table 23) (Walther et al. 2019). References—Larone (1995), Sutton et al. (1998), de Hoog et al. (2000) (morphology), Nguyen et al. (2016, 2017), Walther et al. (2013, 2019), Wagner et al. (2019) (morphology and phylogeny). 98. Phytophthora de Bary, J. Roy. Agric. Soc. England, ser. 2 12: 240 (1876) Background Phytophthora is classified in the kingdom Straminipila within the diploid, alga-like Oomycetes in the Stramenopile clade of the Kingdom Chromista (Cavalier-Smith 1986; Dick 1995; Yoon et al. 2002; Wijayawardene et al. 2020). Phytophthora consists of about 130 described species with many important plant pathogens. The Oomycota are biologically different from main fungal groups within the Kingdom Fungi (Corliss 1994; Cavalier-Smith 1998). For example, their cell walls are made primarily of cellulose instead of chitin as in most fungi and they cannot synthesize β-hydroxysterols, which is vital for synthesizing hormones that regulate sexual reproduction (Hyde et al. 2014). Another important difference is that oomycetes are diploid throughout their life cycle. One similarity between Phytophthora species and Eumycotan fungi is that they both produce hyphae. 13 176 Classification—Oomycota, Peronosporales, Peronosporacae Type species—Phytophthora infestans (Mont.) de Bary Distribution—worldwide Disease symptoms—blight, canker, dieback, root rots and wilt Species can have a large impact on agriculture (e.g. Phytophthora infestans, potato late blight), arbiculture (e.g. Phytophthora ramorum, sudden oak death) and whole ecosystems (e.g. Phytophthora cinnamomi in Australia). Phytophthora species damage plants by killing the tissues and resulting necrosis can be seen in leaves, stems or roots. Some species can cause multiple symptoms on a single host, or cause different symptoms on different hosts (Jung and Blaschke 1996). Blight: Initial symptom is the development of a “watersoaked” appearance, which progresses into brown or black irregular-shaped spots or wedge-shaped lesions. These lesions are usually not surrounded by a yellow halo (Babadoost 2004; Pande et al. 2011; Ali et al. 2017). Canker: A dark discoloured necrotic lesion in the inner bark of a tree can be seen often on the stem or branches. However, generally, cankers are visible once the outer bark is removed. Cankers are often seen with a reddish-brown liquid that oozes through the bark (Davidson et al. 2002; Jung et al. 2018). Dieback: Death of shoot tips, twigs and branch tips can be observed. The infection progresses towards the main stem accompanied by a loss of foliage (Kuske and Benson 1983; Akilli et al. 2013). Decline and Death: This is a gradual process that will take place over several years. Plants fail to grow and the canopy becomes thin due to loss of foliage. Then the whole canopy or sections of the canopy may die (Marais 1980; Belisario et al. 2004; González et al. 2020). Rot: Dark discoloured rotten tissues that are common on roots, but sometimes extend above the soil surface. However, collar rot occurs at the base of the trunk and extends just below the soil line (Jung and Blaschke 1996; Graham et al. 2011; Summerell and Liew 2020). Wilting: This is the first above-ground symptom of root rot. Foliage becomes flaccid due to lack of water intake (Vettraino et al. 2009; Xiong et al. 2019). Phytophthora causes disease in important agricultural and ecological plants. Phytophthora infestans was responsible for the Irish potato famine from 1845 to 1852, causing the death of over 1 million people. Phytophthora ramorum has resulted in the death of millions of coast live oak, tanoak and Japanese larch trees, thus altering the forest ecosystems in California and Oregon, USA (Goheen et al. 2002; Rizzo et al. 2002, 2005). Hosts—Phytophthora agathidicida (commonly known as kauri dieback), which causes kauri death, is considered as one of the world’s most feared fungi (Hyde et al. 2018a). An extensive survey in previously unexplored ecosystems such as natural forests (Rea et al. 2010; Vettraino et al. 2011; Jung et al. 2011, 2017; Reeser et al. 2013), streams (Reeser et al. 2007; Bezuidenhout et al. 2010; Yang et al. 2016; Brazee 13 Fungal Diversity (2020) 103:87–218 et al. 2017), riparian ecosystems (Brasier et al. 2003, 2004; Hansen et al. 2012), and irrigation systems (Hong et al. 2010, 2012; Yang et al. 2014a, b) has led an exponential increase in the number of species. Pathogen biology, disease cycle and epidemiology Morphological based identification and diversity Species-level classification is based on the morphological characterization of reproductive structures including the sporangium (asexual) and oospore (sexual) as well as the production of chlamydospores (Martin et al. 2012). Characteristics that are important for species classification include the diameter of the oogonium and oospore, thickness of the oospore wall, whether or not the oospore fills the oogonium, ornamentation on the oogonial wall, and mode of attachment of the antheridium (Hyde et al. 2014). Identification and classification of Phytophthora species into morphological groups based on several characteristics was initially based on the key provided by Waterhouse (1963), which was later updated by Stamps et al. (1990). Molecular based identification and diversity Phytophthora has been historically placed in the Pythiales with Pythium and related genera, however recent phylogenetic analysis with the large (LSU) or small (SSU) rDNA sequences or cox2 gene has indicated a closer relationship with downy mildew and white rusts (Albugo.) in the Peronosporales (Beakes and Sekimoto 2009; Thines et al. 2009). Additional multigene analyses are vital to clarify the relationship between the Peronosporales and Pythium. Early efforts focusing on the phylogenetic relationships in Phytophthora used nuclear-encoded rDNA, primarily the ITS region (Crawford et al. 1996; Cooke and Duncan 1997; Förster et al. 2000). The first comprehensive study was based on the phylogenetic study of the ITS region (Cooke et al. 2000). The study by Kroon et al. (2004) was based on analysis using two nuclear (tef1, tub2) and two mitochondrial (cox1 and nad1) genes. Subsequent phylogenetic analysis was based on sequences of seven nuclear genetic markers (60S ribosomal protein L10, tub2, enolase, heat shock protein90, large subunit rDNA, TigA gene fusion and tef1) which divided the species into 10 well-supported clades (Blair et al. 2008). The phylogenetic study by Martin et al. (2014) was based on seven nuclear and four mitochondrial genes (cox2, nad9, rps10 and secY). More recently, an extensive study of the genus by Yang et al. (2017) was based on sequences of seven nuclear genetic markers as in Blair et al. (2008). The number of described species in Phytophthora was approximately 55 in 1999, but since then there has been a significant increase in the number of species nearly doubling the number of described species to 105 (Brasier 2007), and over 128 species (Hyde et al. 2014). Additional species have since been described, for example, P. cocois (Weir et al. 2015), P. crassamura (Scanu et al. 2015), P. attenuata, P. Fungal Diversity (2020) 103:87–218 177 Fig. 38 Disease cycle of Phytophthora infestans (redrawn from Bengtsson 2013) xheterohybrida, P. xincrassata (Jung et al. 2017) bringing the total to over 150 species (Jung et al. 2019). The phylogenetic tree constructed is presented in Fig. 39 and the accepted species are given in Table 24. Recommended genetic markers (genus level)—LSU, SSU and cox2 Recommended genetic markers (species level)—LSU, tub2 and cox2 Accepted number of species– There are 317 epithets listed in Index Fungorum (2020), however only 162 species have DNA sequence data (Table 24). References—Waterhouse (1963), Stamps et al. (1990) (morphology); Crawford et al. (1996), Cooke and Duncan (1997), Cooke et al. (2000), Förster et al. (2000), Brasier (2007), Blair et al. (2008) (morphology and phylogeny); Hyde et al. (2014) (phylogeny and accepted species) (Fig. 40). 99. Pythium Pringsh., Jb. wiss. Bot. 1: 304 (1858) Background Pythium is the largest and most comprehensively studied genus in Pythiaceae sensu lato, order Peronosporales sensu lato, class Peronosporomycetes, phylum Oomycota, and kingdom Straminipila (Beakes et al. 2014). Pringsheim (1858) described the genus. However, the initial classification of Pythium has changed many times based on several studies using morphological characteristics (Uzuhashi et al. 2010). Pythium comprises of more than 230 extant species (Hyde et al. 2014), however, identification of species has always been problematic due to limited morphological characters, difficulty in isolating some taxa and lack of molecular data for certain species (Lévesque and de Cock 2004). Classification—Oomycota, Pythiales, Pythiaceae Type species—Pythium monospermum Pr ingsh. (Pringsheim 1858) Distribution—worldwide Disease symptoms—generally cause rot of fruit, roots and stem including pre- or post-emergence damping-off of seeds and seedlings. Pythium causes crown and root rot in mature plants, where plants suddenly wilt during warm and sunny weather and when plants have their first heavy fruit load. Often, upper leaves of infected plants wilt in the day and recover overnight. However, plants eventually die (Craft and Nelson 1996; Postma et al. 2000). The first symptoms of Pythium root infections include stunting. In the root system, initial symptoms are brown to dark-brown lesions on root tips and feeder roots. As the disease progresses, symptoms are soft, brown, stubby roots and lack of feeder roots. In larger roots, the outer root tissue or cortex peels away, leaving the string-like vascular bundles underneath (Postma et al. 2000; Moorman et al. 2002; Al-Mahmooli et al. 2015). Pythium rot also occurs in the crown at the stem base. In cucumber, diseased crowns turn orange-brown, often with a soft rot at the base, while in strawberry seedling roots have dark brown, water-soaked rot and rotten crowns (Columbia and English 1988; Ishiguro et al. 2014). Several species of Pythium cause blight of turfgrass, which initially appears as “greasy” water-soaked areas, but later turn brown and grey (Vencelli and Powell 2008). 13 178 Fig. 39 Maximum likelihood of Phytophthora based on the concatenated seven nuclear genetic markers (60S Ribosomal protein L10 (60S), beta-tubulin (tub), elongation factor 1 alpha (tef1), enolase (Enl), heat shock protein 90 (hsp90), 28S ribosomal DNA (28S), and tigA gene fusion protein (TigA)). ML bootstrap support values over 60% are indicated and BYPP ≥ 0.90 are shown respectively near the nodes. The type species are in bold. Scale bar indicates number of substitutions per site. The tree was rooted with Phytopythiumvexansand Pythium undulatumas as the our group. Likelihood of the best scoring ML tree was − 114471.902046. Estimated base frequencies were as follows: A = 0.216570, C = 0.275568, G = 0.312230, T = 0.195632; substitution rates AC = 0.414835, AG = 1.176570, AT = 0.600142, CG = 0.970565, CT = 5.227735, GT = 1.000000 13 Fungal Diversity (2020) 103:87–218 Fungal Diversity (2020) 103:87–218 179 Fig. 39 (continued) 13 180 Table 23 DNA barcodes available for Mucor Fungal Diversity (2020) 103:87–218 Species Isolate ITS LSU Mucor abundans CBS 388.35 CBS 521.66 CBS 993.70* CBS 126943 CBS 763.74 CBS 210.80* CBS 202.28* CBS 846.73* CBS 526.68 CBS 292.63* CBS 251.53* CBS 293.63* URM 7322 B5-2 CBS 108.16 CBS 293.66 CBS 156.51* ATCC MYA-4767* CBS 385.95* CBS 141.20 CBS 251.35* CBS 230.35* CBS 893.73 EML-PUKI06-1 CBS 132.22 CBS 230.29 CBS 336.68* CBS 566.91* CBS 114.08* CBS 404.71 CBS 174.27* CBS 338.74 CBS 405.58 CBS 242.35 CBS 115.18 CBS 255.36 CBS 226.29* CBS 977.68 EML-PUKI12-1 CBS 154.69 EML-QT1* EML-QT2 CBS 638.74 CBS 143.85* CBS 243.35 CBS 215.27* URM-7908 CBS 586.67* CBS 444.65* CBS 999.70* JN206111 JN206110 NG_063979 JN206457 JN206461 MH875788 NG_057877 JN206504 JN206418 M. aligarensis M. ambiguus M. amphibiorum M. ardhlaengiktus M. atramentarius M. amethystinus M. azygosporus M. bacilliformis M. bainieri M. caatinguensis M. circinelloides M. ctenidius M. durus M. ellipsoideus M. endophyticus M. exponens M. falcatus M. flavus M. fragilis M. fuscus M. fusiformis M. gigasporus M. genevensis M. guiliermondii M. heterogamus M. hiemalis M. inaequisporus M. indicus M. irregularis M. japonicus M. koreanus M. lanceolatus M. laxorrhizus M. luteus M. megalocarpus M. merdophylus M. minutus M. moelleri M. mousanensis 13 MH864344 NR_103615 NR_152960 MH854979 JN206014 JN206015 NR_103639 NR_145285 NR_103628 KT876701 JN205954 MH858796 NR_145295 NR_111683 NR_111661 MH854686 NR_103647 JN206061 KY047147 JF723619 JN206204 NR_111660 NR_103646 HM623318 JN206042 NR_103636 JN206169 JN206167 JN206134 JN206127 JN206177 NR_077173 JX976259 KY047151 JN206158 KT936259 KT936260 JN206205 NR_103642 JX976254 NR_145286 MK775467 JN206048 MH858663 NR_103629 JN206426 NG_057928 NG_057916 JN206424 NG_060334 JN206417 NG_057918 NG_042602 NG_057970 JN206441 NG_057931 JN206464 JN206465 NG_057915 NG_057926 NG_057923 JN206488 NG_057929 NG_057878 JN206446 JN206443 NG_057914 NG_057925 MK775466 JN206463 NG_057875 NG_057912 Fungal Diversity (2020) 103:87–218 Table 23 (continued) 181 Species # M. mucedo M. multiplex M. nidicola M. odoratus M. parviseptatus M. piriformis# M. plasmaticus M. plumbeus M. prayagensis M. pseudolusitanicus M. pseudocircinelloides M. saturninus M. stercorarius# M. strictus M. racemosus M. ramosissimus M. silvaticus M. ucrainicus M. variisporus M. variicolumellatus M. velutinosus M. zonatus M. zychae Ellisomyces anomalus Isolate ITS LSU CBS 542.66* JN206086 JN206480 CBS 987.68 CBS 110662* EML-SBD1 EML-SBD2 CBS 130.41* CBS 417.77 CBS 169.25* CBS 275.49 CBS 634.74 CBS 652.78 CBS 540.78* CBS 543.80 CBS 541.78 CBS 974.68* CNUFC-UK2-1* CNUFC-UK2-2 CBS 100.66* CBS 260.68* CBS 135.65* CBS 249.35 CBS 674.88 CBS 837.70* CBS 236.35* SF012536 UTHSC-04-1961 CBS 148.69* CBS 416.67* CBS 243.57* CBS 697.76 JN206089 NR_111662 KY047148 KY047149 NR_145287 JN206108 NR_103630 JN206480 NG_057924 HM999955 JN206189 MF495059 MF495060 JN206013 NR_103635 KX839689 KX839680 JN206035 NR_126135 NR_103627 JN206122 JN206192 NR_152951 JN205979 MF495054.1 JF299208 NR_103638 NR_103641 NR_145284 JN205993 NG_057927 JN206453 NG_057874 JN206483 HM849677 JN206498 JN206431 JN206458 JN206477 NG_055727 NG_056280 JN206455 JN206507 NG_057972 JN206422.1 NG_057917 NG_057930 NG_067365 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # Several Pythium species are capable of causing fruit rot in numerous crops (Martin and Loper 1999). Pythium fruit rot is commonly known as a cottony leak or watery rot and occurs during wet weather or in poorly drained areas of fields (Ho and Abd-Elsalam 2020; Sharma et al. 2020a). Initial symptoms of the fruit rot are brownish, water-soaked lesions that quickly become large, watery, soft and rotten. The rot generally begins on the parts of fruit in contact with the soil. In cucumber, a brown to dark green blister can be seen on fruit before they become watery and rot. Later, white cottony mycelium can be seen on rotten tissues, especially during humid weather. Pythium fruit rot is most severe in poorly-drained fields during wet weather. The disease can render fruit unmarketable (Ho 2009; Sharma et al. 2020a). Pre-emergence damping-off causes seeds and young seedlings to rot before they emerge from the growing medium in greenhouses, while post-emergence damping-off kills newly emerged seedlings. In the latter, the pathogen causes a watersoaked, soft brown lesion at the stem base, near the soil line, that pinches off the stem causing the seedling to topple over and die (Weiland et al. 2012). Hosts—Pythium has a wide range of hosts including species of Cucurbitaceae and Poaceae, Ananas comosus, Arachis hypogaea, Brassica sp., Carica papaya, Beta vulgaris, Daucus carota subsp. sativus, Dendrobium sp, Solanum sp. and Zingiber officinale. Some species are pathogens of algae, fungi, other oomycetes, nematodes, insects, animals and humans (Van der Plaäts-Niterink1981; Czeczuga et al. 2005; Kawamura et al. 2005; Hwang et al. 2009; Li et al. 2010; Weiland et al. 2012; Ho 2013; Hyde et al 2014). Several species inhabit different soils in cultivated and uncultivated fields including forest (Uzuhashi et al 2010). Pythium arrhenomanes, P. dissotocum, P. elongatum, P. myriotylum, and P. spinosum are important pathogens of rice seedlings (Hendrix 13 182 Fungal Diversity (2020) 103:87–218 Table 24 DNA barcodes available for Phytophthora Species Strain 60S tub2 tef1 Enl HSP90 28S TigA Phytophthora ×alni P. ×heterohybrida P. ×incrassata P. ×stagnum# P. acerina# P. aff. brassicae# P. aff. citrophthora# P. aff. erythroseptica P. aff. hedraiandra# P. aff. himalsilva P. aff. parsiana# P. agathidicida# P. alticola P. amnicola P. andina# P. aquimorbida P. arenaria P. asiatica P. asparagi# P. attenuata P. austrocedrae P. bilorbang# P. bisheria P. boehmeriae# P. borealis P. botryosa# P. brassicae# P. cactorum# P. cajani# P. cambivora# P. capensis P. capsici# P. captiosa# P. castaneae P. chrysanthemi# P. cichorii P. cinnamomi# P. citricola# P. citrophthora# P. clandestina P. cocois P. colocasiae# P. constricta P. crassamura P. cryptogea# P. dauci P. drechsleri# P. elongata P. erythroseptica P. europaea# 47A8 67C1 67C2 36J7 61H1=CBS 133931 CBS 112968 IMI 342898 33A1=P207 33F4=P226 61G4=CBS 128754 47C8 67D5=ICMP 17027 47G5=CBS 121939 61G6=CBS 131652 P13365 40A6=MYA-4578 55C2=CBS 127950 45G1=ATCC 90455 33D7= IMI384046 67C5 41B5=MYA-4073 61G8=CBS 131653 29D2 45F9=CBS 291.29 60B2=CBS 132023 IMI130422=P6945 29D8=CBS 686.95 22E6=P10194 45F6=ATCC 44389 22F6=ATCC 46719 62C1=CBS 128319 22F4=ATCC 15399 46H8=NZFS 430 22H6=MYA-4060 61F1=CBS 123163 62A8=CBS 115029 23B2=ATCC 15401 33H8=ATCC 60440 26H3 32G1=CBS 347.86 67D6=ICMP 16948 22F8=MYA-4159 55C3=CBS 125801 66C9=PH094 61H9=CBS 113.19 32E6=P10728 P10331 33J3=SG1-1 952 61J2=CBS 129.23 62A2=CBS 109049 KX251595 KX251637 KX251644 KX251368 KX250712 EU079880 EU080384 KX251979 KX250411 KX250621 KX252397 KX251076 KX251006 KX251167 EU080182 KX252238 KX251013 KX251651 KX251466 KX251609 KX252161 KX251181 KX250873 EU080161 KX251187 EU079934 KX251993 KX250369 KX251679 KX251494 KX250726 KX250635 KX252554 KX251083 KX252266 KX252007 KX251804 KX250747 KX250551 EU079866 KX251104 KX250558 KX252561 KX251194 KX251867 KX252028 EU079506 KX250880 KX251895 KX251522 KX251596 KX251638 KX251645 KX251369 KX250713 EU079881 EU080385 KX251980 KX250412 KX250622 KX252398 KX251077 KX251007 KX251168 EU080183 KX252239 KX251014 KX251652 KX251467 KX251610 KX252162 KX251182 KX250874 EU080162 KX251188 EU079935 KX251994 KX250370 KX251680 KX251495 KX250727 KX250636 KX252555 KX251084 KX252267 KX252008 KX251805 KX250748 KX250552 EU079867 KX251105 KX250559 KX252562 KX251195 KX251868 KX252029 EU079507 KX250881 KX251896 KX251523 KX251597 KX251639 KX251646 KX251370 KX250714 EU079882 EU080386 KX251981 KX250413 KX250623 KX252399 KX251078 KX251008 KX251169 EU080184 KX252240 KX251015 KX251653 KX251468 KX251611 KX252163 N/A KX250875 EU080163 KX251189 EU079936 KX251995 KX250371 KX251681 KX251496 KX250728 KX250637 KX252556 KX251085 KX252268 KX252009 KX251806 KX250749 KX250553 EU079868 KX251106 KX250560 KX252563 KX251196 KX251869 KX252030 EU079508 KX250882 KX251897 KX251524 KX251598 KX251640 KX251647 KX251371 KX250715 EU079883 EU080387 KX251982 KX250414 KX250624 KX252400 KX251079 KX251009 KX251170 EU080185 KX252241 KX251016 KX251654 KX251469 KX251612 KX252164 KX251183 KX250876 EU080164 KX251190 EU079937 KX251996 KX250372 KX251682 KX251497 KX250729 KX250638 KX252557 KX251086 KX252269 KX252010 KX251807 KX250750 KX250554 EU079869 KX251107 KX250561 KX252564 KX251197 KX251870 KX252031 EU079509 KX250883 KX251898 KX251525 KX251599 KX251641 KX251648 KX251372 KX250716 EU079884 EU080388 KX251983 KX250415 KX250625 KX252401 KX251080 KX251010 KX251171 EU080186 KX252242 KX251017 KX251655 KX251470 KX251613 KX252165 KX251184 KX250877 EU080165 KX251191 EU079938 KX251997 KX250373 KX251683 KX251498 KX250730 KX250639 KX252558 KX251087 KX252270 KX252011 KX251808 KX250751 KX250555 EU079870 KX251108 KX250562 KX252565 KX251198 KX251871 KX252032 EU079510 KX250884 KX251899 KX251526 KX251600 KX251642 KX251649 KX251373 KX250717 EU079885 EU080389 KX251984 KX250416 KX250626 KX252402 KX251081 KX251011 KX251172 EU080187 KX252243 KX251018 KX251656 KX251471 KX251614 KX252166 KX251185 KX250878 EU080166 KX251192 EU079939 KX251998 KX250374 KX251684 KX251499 KX250731 KX250640 KX252559 KX251088 KX252271 KX252012 KX251809 KX250752 KX250556 EU079871 KX251109 KX250563 KX252566 KX251199 KX251872 KX252033 EU079511 KX250885 KX251900 KX251527 KX251601 KX251643 KX251650 KX251374 KX250718 EU079886 EU080390 KX251985 KX250417 KX250627 N/A KX251082 KX251012 KX251173 EU080188 KX252244 KX251019 KX251657 KX251472 KX251615 KX252167 KX251186 KX250879 EU080167 KX251193 EU079940 KX251999 KX250375 KX251685 KX251500 KX250732 KX250641 KX252560 KX251089 KX252272 KX252013 KX251810 KX250753 KX250557 EU079872 KX251110 KX250564 KX252567 KX251200 KX251873 KX252034 EU079512 KX250886 KX251901 KX251528 13 Fungal Diversity (2020) 103:87–218 183 Table 24 (continued) Species # P. fallax P. flexuosa P. fluvialis P. foliorum# P. formosa P. fragariae# P. fragariaefolia P. frigida# P. gallica P. gemini P. gibbosa P. glovera P. gonapodyides# P. gondwanensis P. gregata# P. hedraiandra# P. heveae# P. hibernalis# P. himalsilva P. hydrogena P. hydropathica# P. idaei P. ilicis# P. infestans# P. inflata# P. insolita# P. intercalaris P. intricata P. inundata# P. ipomoeae# P. iranica# P. irrigata P. kernoviae P. lactucae P. lacustris# P. lateralis# P. lilii P. litoralis P. macilentosa P. macrochlamydospora# P. meadii# P. medicaginis# P. megakarya# P. megasperma# P. melonis# P. mengei P. mexicana P. mirabilis P. mississippiae P. morindae Strain 60S tub2 tef1 Enl HSP90 28S TigA 46J2=P10722 67C3 55B6=CBS 129424 49J8=CBS 121655 67C4 22G6=ATCC 11374 61H4=CBS 135747 47G7 50A1=CBS 111474 46H1=CBS 123382 55B7 31E5 21J5=ATCC 46726 22G7 55B8 38C2 22J1=IMI 180616 32F7=CBS 114104 61G3=CBS 128753 46A3 05D1 34D4=CBS 971.95 23A7=ATCC 56615 27A8 28D1 38E1=CBS 691.79 48A1 67B9 P8619 31B6=P10227 61J4=CBS 374.72 04E4 46C8=P10956 61F4 IMI389725=P10337 22H9 CBS 135746 55B9=CBS 127953 58A5 G231E9=IMI 351473 22G5 23A4 61J5=CBS 238.83 62C7=CBS 402.72 41B4 42B2 45G4=CBS 554.88 30C2=ATCC 64070 57J1 62B5=CBS 121982 KX252568 KX251616 KX251208 KX252112 KX251623 KX251529 KX251853 KX250908 KX252589 KX251125 KX251215 KX250642 KX251229 KX252603 KX251243 KX250390 KX251111 KX252126 KX250579 KX252280 KX252294 EU080129 KX250936 KX250474 KX250761 EU080175 KX252617 KX251630 EU080202 EU080844 KX250439 KX252308 EU080041 KX252042 EU080530 KX252133 AB856779 KX251278 KX252329 EU080658 KX250586 KX251902 KX251034 KX251285 KX251700 KX250656 KX250670 KX250488 KX251291 KX252633 KX252569 KX251617 KX251209 KX252113 KX251624 KX251530 KX251854 KX250909 KX252590 KX251126 KX251216 KX250643 KX251230 KX252604 KX251244 KX250391 KX251112 KX252127 KX250580 KX252281 KX252295 EU080130 KX250937 KX250475 KX250762 EU080176 KX252618 KX251631 EU080203 EU080845 KX250440 KX252309 EU080042 KX252043 EU080531 KX252134 AB856782 KX251279 KX252330 EU080659 KX250587 KX251903 KX251035 KX251286 KX251701 KX250657 KX250671 KX250489 KX251292 KX252634 KX252570 KX251618 KX251210 KX252114 KX251625 KX251531 KX251855 KX250910 KX252591 KX251127 KX251217 KX250644 KX251231 KX252605 KX251245 KX250392 KX251113 KX252128 KX250581 KX252282 KX252296 EU080131 KX250938 KX250476 KX250763 EU080177 KX252619 KX251632 EU080204 EU080846 KX250441 KX252310 EU080043 KX252044 EU080532 KX252135 AB856788 KX251280 KX252331 EU080660 KX250588 KX251904 KX251036 KX251287 KX251702 KX250658 KX250672 KX250490 KX251293 KX252635 KX252571 KX251619 KX251211 KX252115 KX251626 KX251532 KX251856 KX250911 KX252592 KX251128 KX251218 KX250645 KX251232 KX252606 KX251246 KX250393 KX251114 KX252129 KX250582 KX252283 KX252297 EU080132 KX250939 KX250477 KX250764 EU080178 KX252620 KX251633 EU080205 EU080847 KX250442 KX252311 EU080044 KX252045 EU080533 KX252136 AB856791 KX251281 KX252332 N/A KX250589 KX251905 KX251037 KX251288 KX251703 KX250659 KX250673 KX250491 KX251294 KX252636 KX252572 KX251620 KX251212 KX252116 KX251627 KX251533 KX251857 KX250912 KX252593 KX251129 KX251219 KX250646 KX251233 KX252607 KX251247 KX250394 KX251115 KX252130 KX250583 KX252284 KX252298 EU080133 KX250940 KX250478 KX250765 EU080179 KX252621 KX251634 EU080206 EU080848 KX250443 KX252312 EU080045 KX252046 EU080534 KX252137 AB856794 KX251282 KX252333 EU080661 KX250590 KX251906 KX251038 KX251289 KX251704 KX250660 KX250674 KX250492 KX251295 KX252637 KX252573 KX251621 KX251213 KX252117 KX251628 KX251534 KX251858 KX250913 KX252594 KX251130 KX251220 KX250647 KX251234 KX252608 KX251248 KX250395 KX251116 KX252131 KX250584 KX252285 KX252299 EU080134 KX250941 KX250479 KX250766 EU080180 KX252622 KX251635 EU080207 EU080849 KX250444 KX252313 EU080046 KX252047 EU080535 KX252138 AB856797 KX251283 KX252334 EU080662 KX250591 KX251907 KX251039 KX251290 KX251705 KX250661 KX250675 KX250493 KX251296 KX252638 KX252574 KX251622 KX251214 KX252118 KX251629 KX251535 KX251859 KX250914 KX252595 KX251131 KX251221 KX250648 KX251235 KX252609 KX251249 KX250396 KX251117 KX252132 KX250585 KX252286 KX252300 EU080135 KX250942 KX250480 KX250767 EU080181 KX252623 KX251636 EU080208 EU080850 KX250445 KX252314 KX252631 KX252048 EU080536 KX252139 AB856800 KX251284 KX252335 EU080663 KX250592 KX251908 KX251040 N/A KX251706 KX250662 KX250676 KX250494 KX251297 KX252639 13 184 Fungal Diversity (2020) 103:87–218 Table 24 (continued) Species # P. multivesiculata P. multivora# P. nagaii P. nemorosa P. nicotianae# P. niederhauserii# P. obscura P. occultans# P. ornamentata P. pachypleura# P. palmivora# P. parsiana# P. parvispora# P. phaseoli P. pini# P. pinifolia P. pisi P. pistaciae# P. plurivora# P. pluvialis# P. polonica P. primulae# P. pseudocryptogea# P. pseudosyringae# P. pseudotsugae P. psychrophila P. quercetorum P. quercina# P. quininea P. ramorum# P. richardiae P. riparia P. rosacearum P. rubi P. sansomeana# P. siskiyouensis# P. sojae# P. sp. brasiliensis P. sp. canalensis P. sp. citricola VIII P. sp. cuyabensis P. sp. delaware P. sp. kelmania P. sp. lagoariana P. sp. personii P. sp. sulawesiensis P. stricta P. syringae# P. taxon parsley P. taxon walnut 13 Strain 60S tub2 tef1 Enl HSP90 28S TigA 30D4 55C5=CBS 124094 61H5=CBS 133248 28J3 22F9=ATCC 15410 01D5 60E9=CBS 129273 65B9=CBS 101557 66D2=CBS 140647 61H8 22G9 47C3=IMI 395329 30G9 35B6 22F1 47H1=CBS 122924 60A4 33D6=IMI 386658 22E9 60B3 40G9 29E9=CBS 620.97 ATCC52402 30A8=CBS 111772 ATCC52938 29J5=CBS 803.95 15C8 30A4=CBS 783.95 45F2=CBS 406.48 32G2 45F5=CBS 240.3 60B1=CBS 132024 22J9 30D7 47H5 41B7=CBS 122779 22D8=CBS 312.62 ATCC46705=P0630 P10456 27D9 P8213 63H4 24A7 60B4=P8220 P11555 P6306 58A2 23A6 61G1=BPIC 2584 40A7 KX250922 KX250775 KX251860 KX250957 KX250509 KX251714 KX252175 KX250600 KX251319 KX250796 KX251055 KX252357 KX251818 KX250502 KX250803 KX251333 KX251735 KX251748 KX250817 KX250971 KX252532 KX252063 EU080626 KX250978 EU080426 KX250992 KX251069 KX252647 EU080107 KX252147 KX251923 KX251347 KX251431 KX251550 KX251944 KX250677 KX251762 EU080419 EU079569 KX250838 EU080664 KX251396 KX251986 EU080358 EU080312 EU080345 KX252217 KX252203 KX252105 KX251452 KX250923 KX250776 KX251861 KX250958 KX250510 KX251715 KX252176 KX250601 KX251320 KX250797 KX251056 KX252358 KX251819 KX250503 KX250804 KX251334 KX251736 KX251749 KX250818 KX250972 KX252533 KX252064 EU080627 KX250979 EU080427 KX250993 KX251070 KX252648 EU080108 KX252148 KX251924 KX251348 KX251432 KX251551 KX251945 KX250678 KX251763 EU080420 EU079570 KX250839 EU080665 KX251397 KX251987 KX252502 EU080313 N/A KX252218 KX252204 KX252106 KX251453 KX250924 KX250777 KX251862 KX250959 KX250511 KX251716 KX252177 KX250602 KX251321 KX250798 KX251057 KX252359 KX251820 KX250504 KX250805 KX251335 KX251737 KX251750 KX250819 KX250973 KX252534 KX252065 EU080628 KX250980 EU080428 KX250994 KX251071 KX252649 EU080109 KX252149 KX251925 KX251349 KX251433 KX251552 KX251946 KX250679 KX251764 EU080421 EU079571 KX250840 EU080666 KX251398 KX251988 EU080359 EU080314 EU080346 KX252219 KX252205 KX252107 KX251454 KX250925 KX250778 KX251863 KX250960 KX250512 KX251717 KX252178 KX250603 KX251322 KX250799 KX251058 KX252360 KX251821 KX250505 KX250806 KX251336 KX251738 KX251751 KX250820 KX250974 KX252535 KX252066 EU080629 KX250981 EU080429 KX250995 KX251072 KX252650 N/A KX252150 KX251926 KX251350 KX251434 KX251553 KX251947 KX250680 KX251765 EU080422 EU079572 KX250841 EU080667 KX251399 KX251989 EU080360 EU080315 EU080347 KX252220 KX252206 KX252108 KX251455 KX250926 KX250779 KX251864 KX250961 KX250513 KX251718 KX252179 KX250604 KX251323 KX250800 KX251059 KX252361 KX251822 KX250506 KX250807 KX251337 KX251739 KX251752 KX250821 KX250975 KX252536 KX252067 EU080630 KX250982 EU080430 KX250996 KX251073 KX252651 KX252522 KX252151 KX251927 KX251351 KX251435 KX251554 KX251948 KX250681 KX251766 EU080423 EU079573 KX250842 EU080668 KX251400 KX251990 EU080361 EU080316 EU080348 KX252221 KX252207 KX252109 KX251456 KX250927 KX250780 KX251865 KX250962 KX250514 KX251719 KX252180 KX250605 KX251324 KX250801 KX251060 KX252362 KX251823 KX250507 KX250808 KX251338 KX251740 KX251753 KX250822 KX250976 KX252537 KX252068 EU080631 KX250983 EU080431 KX250997 KX251074 KX252652 EU080110 KX252152 KX251928 KX251352 KX251436 KX251555 KX251949 KX250682 KX251767 EU080424 EU079574 KX250843 EU080669 KX251401 KX251991 EU080362 EU080317 EU080349 KX252222 KX252208 KX252110 KX251457 KX250928 KX250781 KX251866 KX250963 KX250515 KX251720 KX252181 KX250606 KX251325 KX250802 KX251061 KX252363 KX251824 KX250508 KX250809 KX251339 KX251741 KX251754 KX250823 KX250977 KX252538 KX252069 N/A KX250984 EU080432 KX250998 KX251075 KX252653 KX252523 KX252153 KX251929 KX251353 KX251437 KX251556 KX251950 KX250683 KX251768 EU080425 N/A KX250844 EU080331 KX251402 KX251992 EU080363 EU080318 EU080350 KX252223 KX252209 KX252111 KX251458 Fungal Diversity (2020) 103:87–218 185 Table 24 (continued) Species Strain 60S tub2 tef1 Enl HSP90 28S TigA P. taxon-aquatilis P. taxon-castitis P. taxon-emzansi P. tentaculata# P. terminalis P. thermophila P. trifolii P. tropicalis# P. uliginosa P. vignae# P. virginiana 38J5 61E7=CBS 131246 61F2 29F2=CBS 552.96 65B8=CBS 133865 55C1=CBS 127954 29B2 35C8=CBS 434.91 62A3=CBS 109054 45G9=ATCC 64832 44G6 KX250929 KX252098 KX250859 EU079955 KX250607 KX251354 KX251951 KX250698 EU080011 KX251783 KX252371 KX250930 KX252099 KX250860 EU079956 KX250608 KX251355 KX251952 KX250699 EU080012 KX251784 KX252372 KX250931 KX252100 KX250861 EU079957 KX250609 KX251356 KX251953 KX250700 EU080013 KX251785 KX252373 KX250932 KX252101 KX250862 EU079958 KX250610 KX251357 KX251954 KX250701 KX251571 KX251786 KX252374 KX250933 KX252102 KX250863 EU079959 KX250611 KX251358 KX251955 KX250702 KX251572 KX251787 KX252375 KX250934 KX252103 KX250864 EU079960 KX250612 KX251359 KX251956 KX250703 EU080015 KX251788 KX252376 KX250935 KX252104 KX250865 EU079961 KX250613 KX251360 KX251957 KX250704 KX251573 KX251789 KX252377 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains and voucher strains are in bold. Species confirmed with pathogenicity studies are marked with #. (VdPN) are strains used by Van der Plaäts-Niterink (1981) for descriptions Fig. 40 Disease cycle of a Pythium species (redrawn from van West et al. 2003) and Campbell 1973; Hsieh 1978; Ventura et al. 1981; Chun and Schneider 1998; Eberle et al. 2007; Kreye et al. 2009; Oliva et al. 2010; Banaay et al. 2012; Van Buyten and Höfte 2013). Pythium insidiosum causes pythiosis in mammals including humans (van der Plaäts-Niterink 1981; de Cock et al. 1987). Some species target below-ground plant parts and some species can cause fruit rot, however, some Pythium species can also benefit plants as endophytes by acting as biocontrol agents (Benhamou et al. 1997) and by stimulating plant growth (Martin and Loper 1999; Mazzola et al. 2002). Pathogen biology, disease cycle and epidemiology Pythium species grow and colonize a plant by producing hyphae which extract nutrients from the host. Once the hyphae from opposite mating types meet, they produce thick-walled oospores which serve as overwintering structures. Upon germination, an oospore may produce more hyphae, or develop a zoosporangium, which produces motile zoospores that swim to and infect plants. Zoosporangia can also germinate and directly infect plants (Ho 2009; van West et al. 2003). 13 186 Morphological based identification and diversity Pythium has hyaline hyphae which are coenocytic without cross septa (van der Plaäts-Niterink 1981). Filamentous and globose sporangia are present, and zoospores develop in a vesicle, which is formed at the tip of a discharge tube from a sporangium. After fertilization with paragynous or hypogynous antheridia, oospores are formed in smooth or ornamented oogonia. The oospore can fill the whole organism or can have space between the walls of the oogonia and oospore. The process of zoospore formation within a vesicle is a characteristic feature of the genus, which distinguishes it from morphologically similar genera such as Phytophthora and Halophytophthora. However, the formation of zoospores is similar to Lagenidium, which features endobiotic and holocarpic features not observed in Pythium (Dick 2001). Species delimitation based on morphological characteristics such as shape and size of sporangia and oogonia is difficult as these characteristics are often shared among different species. Molecular based identification and diversity Lévesque and de Cock (2004) separated the genus into 11 clades (A-K) using phylogenies of ITS and 28S. Clade K, which includes P. vexans was transferred to a new genus Phytopythium with Phytopythium sindhum as type species (Bala et al. 2010), while the remaining clades can be divided into two groups: species with filamentous sporangia (clades A-D) and species with globose sporangia (clades E–J). Identification of Pythium isolates to species level is recommended based on cox1 and ITS gene regions. The use of ITS region alone cannot accurately identify all Pythium species. Several species are indistinguishable based on both ITS and cox1 sequences. Lévesque and de Cock (2004) provided the first extensive study of Pythium, accepting 116 species. Additional species have recently been described for example P. alternatum (Rahman et al. 2015), P. biforme, P. brachiatum, P. junctum, P. utonaiense (Uzuhashi et al. 2015), P. cedri (Chen et al. 2017), P. heteroogonium, P. longipapillum, P. oryzicollum (Salmaninezhad and Mostowfizadeh-Ghalamfarsa 2019). Currently, there are more than 130 accepted species in the genus (Arafa et al. 2020). The phylogenetic tree constructed is presented in Fig. 41 and the information of species are given in Table 25. Recommended genetic markers (generic level within Pythium sensu lato)—18S (small subunit, SSU) and 28S (large subunit, LSU) nuclear rRNA genes Recommended genetic markers (sub-generic, inter- and intra-specific level)—The internal transcribed spacers (ITS including ITS1, 5.8S rRNA, and ITS2), cytochrome c oxidase subunit 2 (cox2) Accepted number of species—There are 330 epithets listed in Index Fungorum (2020), however only 157 species have DNA sequence data (Table 25). 13 Fungal Diversity (2020) 103:87–218 References—van der Plaäts-Niterink (1981), Dick (2001) (morphology), Lévesque and de Cock (2004), Hyde et al. (2014), Arafa et al. (2020) (phylogeny and accepted species numbers) 100. Rhizopus Ehrenb., Nova Acta Phys.-Med. Acad. Caes. Leop.-Carol. Nat. Cur. 10: 198 (1821) Background Rhizopus is classified in the subphylum Mucoromycotina, class Mucoromycetes, order Mucorales and family Rhizopodaceae (Wijayawardene et al, 2018, 2020). The genus is one of the most diverse and constitutes an important genus within the order Mucorales. Rhizopus species are common post-harvest pathogens of fruits, vegetables, crops and stored foods, while some Rhizopus species are human pathogens. Rhizopus arrhizus and Rhizopus microsporus can cause mucoromycosis in immunocompromised humans (Yildirim et al. 2010; Benedict and Brandt 2016). Morphology-based (size of sporangia and sporangiophores, and rhizoids) and physiology-based (growth temperature) identification and classification grouped the genus in three groups: R. microsporus, R. stolonifer, and R. arrhizus (syn: R. oryzae) (Schipper 1984). Schipper (1984) and Schipper and Stalpers (1984), provided the first significant monographs of Rhizopus. Fundamental morphological-based identification was provided which is still widely used in current taxonomic classification for Rhizopus (Schipper 1984; Schipper and Stalpers 1984; Hartanti et al. 2015). The inclusion of DNA-based phylogenetic tools has resulted in significant changes in the taxonomic classification (Vebliza et al. 2018). With the implementation of molecular-based identification, Abe et al. (2006, 2010), Zheng et al. (2007b), and Liu et al. (2007) provided significant contributions in the classification of Rhizopus. Briefly, in current taxonomy Rhizopus arrhizus is a synonym of R. oryzae, R. reflexus to R. lyococcus and Amylomyces rouxii is a synonym of Rhizopus arrhizus (Liu et al. 2007; Hyde et al. 2014; Vebliza et al. 2018) (Fig. 42). Phylogenomic approaches have the potential to provide a clear understanding of the inter-relationships of species (Gryganskyi et al. 2018). In recent revisions, data from wholegenome sequencing have been used (Gryganskyi et al. 2018). Phylogenetic analysis based on a dataset of 192 orthologous protein-coding genes extracted from whole-genome sequencing of representative species provided a robust phylogeny and tree topology for Rhizopus. The phylogenetic analysis resulted in similar tree topology obtained from studies which utilize ITS and pyrG genes or 76 orthologous proteins from the genomes (Liu et al. 2007; Chibucos et al. 2016). In brief, R. microsporus is suggested to be a monophyletic sister clade to other Rhizopus clades, R. stolonifer was found to be sister to R. arrhizus and R. delemar and these four species are monophyletic (Gryganskyi et al. 2010, 2018). A comparative analysis of the mating-type locus across Rhizopus revealed that its structure is flexible even between Fungal Diversity (2020) 103:87–218 187 Fig. 41 Maximum likelihood of Pythium species based on the concatenated SSU, ITS, LSU, cox2 and tub2 regions. The maximum parsimonious dataset consisted of 528 constant, 71 parsimony-informative and 556 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 1637 steps (CI = 0.200, RI = 0.737, RC = 0.147, HI = 0.800). ML and MP bootstrap support values over 60% and BYPP ≥ 0.90 are indicated. Type strains are in bold and the 11 clades (A–K) are indicated. Scale bar indicates number of substitutions per site. The tree was rooted with Lagenidium giganteum (CBS 580.84) and Lagenidium sp. (DAOM 242348 and CBS 127283). Likelihood of the best scoring ML tree was − 28453.969593. Estimated base frequencies were as follows: A = 0.264872, C = 0.163069, G = 0.213432, T = 0.358627; substitution rates AC = 1.219282, AG = 3.062456, AT = 3.113530, CG = 0.855790, CT = 4.379562, GT = 1.000000 13 188 Fig. 41 (continued) 13 Fungal Diversity (2020) 103:87–218 Fungal Diversity (2020) 103:87–218 189 Table 25 DNA barcodes available for Pythium Species Isolate Host SSU ITS Pythium abappressorium# P. acanthicum# P. acanthophoron# P. acrogynum CBS 110198 Triticum aestivum HQ643408 HQ643408 HQ643408 KJ595409 KJ595533 CBS 377.34 CBS 337.29 CBS 549.88 AY598617 AY598711 N/A AY598617 AY598617 KJ595380 AY598711 AY598711 KJ595376 AY598638 AY598638 AB362324 KJ595504 KJ595500 KJ595458 P. adhaerens P. afertile P. alternatum P. amasculinum CBS 520.74 LEV2066 GUCC0015 CBS 552.88 AY598619 N/A N/A AY598671 AY598619 HQ643416 AB998876 AY598671 KJ595386 KJ595440 KJ595390 KJ595510 KJ595563 N/A KJ595514 P. anandrum# P. angustatum# AY598650 AY598623 AY598650 AY598650 AB362328 AY598623 AY598623 KJ595387 KJ595450 KJ595511 Unknown Soil (Vitis sp.) Nymphyoidespeltata Soil Triticum aestivum Zea mays AY598622 HQ643443 AY598631 AY598632 AY598627 AKXY02050628 AY598622 HQ643443 AY598631 AY598632 AY598627 AY598628 AY598622 HQ643443 AY598631 AY598632 AY598627 AY598628 KJ595344 KJ595422 KJ595400 KJ595355 AB507410 AKXY02053172 KJ595472 KJ595547 KJ595524 KJ595481 DQ071297 KJ595451 Prunus serotina Aquatic Soil Aquatic Linumusitatissimum Hordeum vulgare Soil Soil Soil (spoil heap) Soil Turf grass HQ643476 N/A AY598662 N/A AY598659 GQ244426 HQ643482 AY598635 HQ643373 N/A AY598675 HQ643476 KJ995584 AY598662 KJ995581 AY598659 GQ244426 HQ643482 AY598635 HQ643373 HQ643484 AY598675 HQ643476 KJ995601 AY598662 KJ995603 AY598659 GQ244426 HQ665069 AY598635 HQ643373 HQ665111 AY598675 AB512889 N/A EF408876 N/A KJ595368 KJ595433 JX397983 KJ595360 AB690678 KJ595427 KJ595404 AB512822 N/A EF408882 N/A KJ595493 KJ595558 JX397969 KJ595485 KJ595464 KJ595551 KJ595528 P. caudatum# P. cederbergense# P. cedri# P. chamaehyphon# P. chondricola# P. citrinum P. coloratum# P. conidiophorum# P. contiguanum P. cryptoirregulare# CBS 285.31 CBS 522.74 (VdPN) CBS 118.80 CBS 120945 CBS 772.81 CBS 215.80 CBS 263.38 CBS 324.62 (VdPN) DAOM 230386 UZ00796 CBS 551.88 UZ00736 CBS 288.31 CBS 124059 CBS 112353 CBS 222.94 CBS 112544 CBS 122659 CBS 842.68 (VdPN) CBS 584.85 CBS 133716 Chen 30 CBS 259.30 CBS 203.85 CBS 119171 CBS 154.64 CBS 223.88 CBS 221.94 CBS 118731 Solanum tuberosum Ananas sativus Soil (Spinacia oleracea) Soil Turf grass Soil Soil (vegetable garden) Rheum rhaponticum Soil HQ643136 N/A N/A AY598666 N/A HQ643375 AY598633 AY598629 HQ643514 HQ643515 HQ643136 JQ412768 KX423751 AY598666 AY598620 HQ643375 AY598633 AY598629 HQ643514 HQ643515 HQ665277 KJ716864 N/A AY598666 AY598620 HQ643375 AY598633 AY598629 HQ665162 HQ643515 AF290309 JQ412805 N/A AB257280 KJ595354 AB690679 KJ595346 KJ595361 KJ595358 GU071763 KJ595459 JQ412781 N/A KJ595448 KJ595480 KJ595465 KJ595474 KJ595486 KJ595483 GU071888 P. cucurbitacearum# P. cylindrosporum# P. cystogenes# P. debaryanum# P. delawarense P. deliense# P. diclinum# CBS 748.96 CBS 218.94 CBS 675.85 CBS 752.96 CBS 123040 CBS 314.33 CBS 664.79 Xiphinemarivesi Aspalathuslinearis roots of Cedrus Carica papaya Chondruscrispus Soil (Vitis sp.) Soil (tree nursery) Soil Soil (salt marsh) Euphorbia pulcherrima Unknown Soil Viciafaba Tulipa sp. Glycine max Nicotiana tabacum Beta vulgaris AY598667 AY598643 HQ643518 AY598704 KF853241 AY598674 N/A AY598667 AY598643 HQ643518 AY598704 EU339312 AY598674 AY598690 AY598667 AY598643 HQ643518 AY598704 KF853240 AY598674 HQ665282 AB690680 GU071762 KJ595396 KJ595399 KJ595430 KJ595372 KJ595394 KJ595460 GU071877 KJ595520 KJ595523 KJ595555 KJ595497 KJ595518 P. aphanidermatum# P. apiculatum P. apleroticum P. aquatile# P. aristosporum P. arrhenomanes# P. attrantheridium# P. biforme P. boreale P. brachiatum P. buismaniae P. camurandrum P. canariense P. capillosum P. carbonicum# P. carolinianum# P. catenulatum# LSU AY598619 HQ643416 N/A AY598671 cox2 tub2 13 190 Fungal Diversity (2020) 103:87–218 Table 25 (continued) Species # P. dimorphum P. dissimile P. dissotocum# P. echinulatum# P. emineosum P. erinaceum P. ershadii P. flevoense P. folliculosum# P. glomeratum# P. graminicola# P. grandisporangium# P. helicandrum P. helicoides# P. heteroogonium P. heterothallicum# P. hydnosporum# P. hypogynum# P. inflatum# P. insidiosum# P. intermedium# P. irregular# P. iwayamai# P. jasmonium P. junctum P. kashmirense# P. kunmingense# P. litorale# P. longandrum# P. longipapillum# P. longisporangium# P. lucens# P. lutarium# P. lycopersici# P. macrosporum# P. mamillatum# P. marinum# P. marsipium# P. mastophorum# P. megacarpum 13 Isolate Host SSU ITS CBS 406.72 CBS 155.64 CBS 166.68 (VdPN) CBS 281.64 (VdPN) CBS 124057 CBS 505.80 IRAN2379C CBS 234.72 CBS 220.94 CBS 122644 CBS 327.62 Pinus taeda Pinus radiata Triticum aestivum AY598651 AY598681 AY598634 AY598651 AY598651 AB362331 AY598681 AY598681 KJ595347 AY598634 AY598634 KJ595351 KJ595454 KJ595475 KJ595479 Soil (forest nursery) AY598639 AY598639 AY598639 AB362327 KJ595449 N/A N/A N/A AY598691 AY598676 N/A AY598625 GQ244427 AY598694 KT894054 AY598691 AY598676 HQ643542 AY598625 KJ595432 AB362326 KJ595363 N/A KJ595424 AF196593 KJ595557 KJ595456 N/A KJ595488 N/A KJ595548 KJ595452 AY598692 AY598692 AY598692 KJ595367 KJ595492 AY598653 AY598665 N/A AY598654 AY598672 AY598653 AY598665 KX228103 AY598654 AY598672 KJ595453 AB511994 KX228117 AB512850 KJ595489 AY598693 AY598626 HQ643565 HQ665171 AB362325 AY598626 AY598626 KJ595352 KJ595447 N/A AF289981 AY598647 AY598637 AY598637 KJ595391 AY598647 AY598647 AB507410 KJ595515 AB512836 AY598702 AY598648 AY598702 AY598702 GU071760 AY598648 AY598648 JX397979 GU071886 JX397965 HQ643778 N/A HQ643671 AY598700 HQ643386 HQ643778 KJ995576 HQ643671 AY598700 HQ643386 HQ643778 KJ995605 HQ643671 HQ665259 HQ643386 KJ595406 N/A KJ595429 KJ595389 KJ595418 KJ595530 N/A KJ595553 KJ595513 KJ595543 HQ643679 N/A N/A HQ643681 HQ643682 N/A HQ643679 KX228105 HQ643680 HQ643681 HQ643682 HQ643683 HQ665071 N/A HQ665099 HQ643681 HQ665163 HQ665119 KJ595413 KX228130 KJ595426 KJ595415 KJ595359 KJ595343 KJ595538 KX228114 KJ595550 KJ595540 KJ595484 KJ595554 AY598646 AY598703 AY598646 AY598646 AB512916 AY598703 HQ665173 AB362325 AB512842 AB512844 N/A N/A AY598661 AY598689 AY598689 KJ595398 AY598699 HQ665297 KJ595401 AY598661 AY598661 KJ595378 KJ595522 KJ595525 KJ595502 HQ643388 HQ643388 HQ643388 AB690665 KJ595536 Juniperus communis Soil Soil Soil Soil Soil Saccharum officinarum CBS 286.79 Decaying leaf (Zostera marina) CBS 393.54 Rumex acetosella CBS 286.31 Phaseolus vulgaris 079-1 - CBS 141232 Soil CBS 450.67 Soil (Sambucus) CBS 253.60 Unknown (VdPN) CBS 234.94 Soil CBS 168.68 Saccharum offici(VdPN) narum CBS 574.85 Equus ferus CBS 266.38 Agrostis stolonifera (VdPN) CBS 250.28 Phaseolus vulgaris CBS 156.64 Soil (Pinus sp.) (VdPN) CBS 101876 Arabidopsis thaliana UZ00732 Aquatic CBS 122908 Soil CBS 550.88 Soil (Viciafaba) CBS 118360 Soil (Phragmites australis) CBS 112355 Soil NRh8* Soil CBS 122646 Soil (Vitis sp.) CBS 113342 Triticum CBS 222.88 Soil CBS 122909 Soil (Lycopersicum esculentum) CBS 574.80 Flower bulb CBS 251.28 Beta vulgaris (VdPN) CBS 750.96 Soil CBS 773.81 Nymphyoides peltata CBS 375.72 Apiumgraveolens (VdPN) CBS 112351 Soil (Vitis sp.) LSU GQ244427 HQ665243 N/A AY598691 HQ665160 HQ665097 AY598625 AY598653 AY598665 N/A AY598654 AY598672 cox2 AB362329 DQ071377 KX228131 AB512919 KJ595364 tub2 Fungal Diversity (2020) 103:87–218 191 Table 25 (continued) Species P. megalacanthum P. mercurial# Isolate # P. middletonii# P. minus# P. monospermum# P. montanum P. multisporum P. nagaii# P. nodosum# P. nunn# P. oedochilum# P. okanoganense# P. oligandrum# P. oopapillum# P. ornacarpum P. ornamentatum P. orthogonon# P. oryzicollum# P. ostracodes# P. pachycaule# P. paddicum# P. paroecandrum# P. parvum P. pectinolyticum P. periilum# P. periplocum# P. perplexum# P. phragmitis# P. pleroticum P. plurisporium# P. polare# P. polymastum# P. porphyrae# P. phragmiticola P. prolatum# P. pyrioosporum P. pyrilobum# P. radiosum P. recalcitrans# P. rishiriense P. rhizo-oryzae# CBS 101356 CBS 122443 Host Chrysanthemum Macadamia integrifolia CBS 528.74(VdPN) Soil CBS 226.88 Soil CBS 158.73 Soil (VdPN) CBS 111349 Soil (Picea abies) CBS 470.50 Soil CBS 779.96 Soil CBS 102274 Soil CBS 808.96 Soil CBS 292.37 Unknown CBS 315.81 Triticum aestivum CBS 382.34 Viola sp. (VdPN) CBS 124053 Cucumis sativus CBS 112350 Soil CBS 122665 Soil CBS 376.72 Zea mays Kr7 Soil CBS 768.73 Soil (VdPN) CBS 227.88 Soil CBS 698.83 Triticum and Hordeum CBS 157.64 Soil (VdPN) CBS 225.88 Soil CBS 122643 Soil CBS 169.68 Soil (VdPN) CBS 289.31 Citrullus vulgaris CBS 674.85 Viciafaba CBS 117104 Soil (Phragmites australis) CBS 776.81 Nymphyoides peltata CBS 100530 Agrostis CBS 118203 Sanionia uncinata CBS 811.70 Lactuca sativa (VdPN) CBS 369.79 Porphyrayezoensis (VdPN) P56 Soil CBS 845.68 Rhododendron sp. IRAN2382C Soil CBS 158.64 Pinus radiata CBS 217.94 Soil CBS 122440 Soil (Vitis vinifera) GUCC0007 Aquatic CBS 119169 Soil SSU ITS LSU N/A KF853243 HQ643693 KJ716865 DQ916363 KF853236 cox2 tub2 KJ595435 AB690666 N/A KJ595466 N/A HQ643696 HQ643697 AY598640 AY598640 AB362318 HQ643696 HQ665168 AB362320 HQ643697 HQ643697 KJ595350 KJ595457 KJ595446 KJ595478 HQ643389 AY598641 AY598705 N/A AY598709 AY598664 AY598649 AY598618 HQ643389 AY598641 AY598705 HQ643709 AY598709 AY598664 AY598649 AY598618 HQ643389 AY598641 AY598705 HQ665055 AY598709 AY598664 AY598649 AY598618 KJ595410 AB362319 KJ595402 KJ595407 AF196609 AB108011 KJ595373 KJ595381 KJ595534 KJ595455 KJ595526 KJ595531 DQ071325 EF408883 KJ595498 KJ595505 N/A HQ643721 N/A AY598710 N/A AY598663 FJ655174 HQ643721 HQ643722 AY598710 KX228072 AY598663 FJ655174 HQ643721 HQ665117 HQ665221 N/A AY598663 KJ595431 KJ595411 KJ595428 KJ595379 KX228125 AB690668 KJ595556 KJ595535 KJ595552 KJ595503 KX228108 EF408880 AY598687 AY598707 AY598687 HQ665169 KJ595362 AY598707 AY598707 JX397982 KJ595487 JX397968 AY598644 AY598644 AY598644 DQ071391 DQ071332 AY598697 HQ643739 AY598683 AY598697 AY598697 AB362322 HQ643739 HQ643739 N/A AY598683 HQ665141 N/A KJ595445 KJ595469 KJ595444 AY598670 AY598658 HQ643746 AY598670 AY598670 KJ595369 AY598658 AY598658 KJ595395 HQ643746 HQ665081 AJ890351 KJ595494 KJ595519 EU152854 AY598642 AY598684 KJ716858 AY598660 AY598642 AY598684 AB299390 AY598660 AB362321 KJ595405 KJ595417 KJ595403 KJ595461 KJ595529 KJ595542 KJ595527 AY598673 AY598673 AY598673 KJ595377 KJ595501 N/A AY598652 N/A AY598636 N/A N/A N/A HQ643757 KC145165 AY598652 KT894052 AY598636 AY598695 DQ357833 AB998878 HQ643757 KC145167 KJ595462 N/A KJ595477 N/A EF195143 N/A KJ595545 AY598642 AY598684 KJ716859 AY598660 N/A AY598652 N/A AY598636 HQ665156 KJ716861 N/A HQ643757 KC145166 AB362330 KJ595349 KJ595356 KJ595423 KJ595420 13 192 Fungal Diversity (2020) 103:87–218 Table 25 (continued) Species Isolate Host SSU ITS P. rhizosaccharum CBS 112356 N/A HQ643760 HQ665072 AB362323 KJ595463 P. rostratifingens# P. rostratum# P. salpingophorum# CBS 115464 CBS 533.74 CBS 471.50 (VdPN) CBS 129726 CBS 294.37 CBS 112354 CBS 129728 CBS 122490 CBS 119359 CBS 275.67 (VdPN) CBS 462.48 (VdPN) DAOM 240293 CBS 110030 CBS 603.73 CBS 453.67 CBS 122491 LEV1534 CBS 316.33 (VdPN) CBS 323.65 CBS 219.65 Soil (Saccharum officinarum) Soil (Malus sp.) Soil Lupinus angustifolius Glycine max Ipomoea batatas Soil Zea mays Soil (forest) Phaseolus vulgaris Compost HQ643761 AY598696 AY598630 HQ643761 HQ643761 KJ595416 AY598696 AY598696 KJ595388 AY598630 AY598630 KJ595384 KJ595541 KJ595512 KJ595508 N/A AY598680 HQ643772 N/A HQ643773 N/A AY598701 JF836869 AY598680 HQ643772 JF836871 HQ643773 EF688275 AY598701 JF895530 KJ595370 KJ595412 JF895532 AB362317 KJ595421 KJ595366 KJ595470 KJ595495 KJ595537 KJ595471 KJ595467 KJ595546 KJ595491 Unknown AY598655 AY598655 AY598655 AB512921 AB512852 Soil Soil Daucus carota Soil Soil Turfgrass Grass N/A N/A AY598682 AY598645 HQ643854 N/A AY598624 KJ716866 HQ643836 AY598682 AY598645 HQ643854 HQ643855 AY598624 KJ595437 KJ595408 KJ595393 KJ595383 AB362315 KJ595439 KJ595374 KJ595560 KJ595532 KJ595517 KJ595507 KJ595468 KJ595562 KJ595499 Lactuca sativa N/A AY598677 HQ665207 KJ595375 Chenopodium album AKYB02045405 AY598656 AY598656 KJ595357 N/A KJ595482 P. schmitthenneri# P. scleroteichum# P. segnitium P. selbyi# P. senticosum# P. solare P. spinosum# P. splendens# P. stipitatum P. sukuiense P. sulcatum# P. sylvaticum# P. takayamanum P. tardicrescens# P. torulosum# P. tracheiphilum# P. ultimum var. sporangiiferum# P. ultimum var. ultimum# P. uncinulatum# P. undulatum# CBS 398.51 CBS 518.77 CBS 157.69 (VdPN) P. urmianum IRAN2376C P. utonaiense UZ00769 CBS 295.37 P. vanterpoolii# CBS 119.80(VdPN) P. vexans# # CBS 119168 P. viniferum CBS 159.64 P. violae# (VdPN) P. wohlseniorum W15-2 Pythiumsp. rooibos 2 STE-U 7550 LSU KJ716862 AY598680 HQ643772 KJ716863 HQ643773 KJ716860 AY598701 KJ716866 HQ665059 HQ665281 AY598645 HQ643854 HQ643855 AY598624 cox2 tub2 Lepidium sativum AY598657 AY598657 AY598657 KJ595382 KJ595506 Lactuca sativa Soil (Pinus sp.) AY598712 AY598708 AY598712 AY598712 KJ595385 AY598708 AY598708 KJ595348 KJ595509 KJ595476 Soil Aquatic Triticum aestivum Soil Soil (Vitis sp.) Soil N/A N/A AY598685 HQ643400 HQ643956 AY598706 KT894049 KJ995587 AY598685 HQ643400 HQ643956 AY598706 N/A N/A KJ595496 EF426556 KJ595544 JX397966 Aquatic Aspalathus linearis N/A N/A MH277978 MH289800 MH289798 JQ412777 N/A JQ412813 N/A KJ995600 AY598685 HQ643400 HQ643956 AY598706 N/A KJ595371 GU133518 KJ595419 JX397980 MH289799 JQ412789 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains and voucher strains are in bold. Species confirmed with pathogenicity studies are marked with #. (VdPN) are strains used by Van der Plaäts-Niterink (1981) for descriptions different species in the same genus, but shows similarities between Rhizopus and other mucoralean taxa. Variation of the genome size was also noted to be approximately three-fold within a species which are induced by changes in transposable element copy numbers and genome duplications (Gryganskyi et al. 2018). Bruni et al. (2019) successfully adapted the CRISPR-Cas 9 technique for inducing pyrF gene-specific 13 mutations in two strains of R. delemar, the causative agent of mucoromycosis. This new tool is suggested to be useful in investigating the pathogenesis mechanisms of R. delemar and also generating specific mutants of Mucorales fungi. Classification—Mucoromycota, Mucoromycotina, Mucoromycetes, Mucorales, Rhizopodaceae Fungal Diversity (2020) 103:87–218 193 Fig. 42 Phylogenetic tree generated by maximum likelihood analysis of combined ITS- LSUSSU sequence data of Rhizopus, Backusella and Mucor species. Twenty-six taxa containing 2600 characters including gaps were used in the phylogenetic analysis. The tree was rooted using Backusella circina (CBS 128.70) and Mucor indicus (CBS 226.29). The best scoring RAxML tree with a final likelihood value of − 11138.113172 is presented. The matrix contained 761 distinct alignment patterns, with 41.20% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.293528, C = 0.180262, G = 0.236482, T = 0.289728; substitution rates AC = 0.787730, AG = 2.127667, AT = 1.579251, CG = 0.715792, CT = 3.683423, GT = 1.000000; gamma distribution shape parameter α = 0.181944.ML bootstrap support values greater than 70% are shown near the nodes. The type species are in bold. Scale bar indicates the number of substitutions per site Type species—Rhizopus stolonifera (Ehrenb.) Vuill. 1902 Distribution—worldwide Disease symptoms—Rhizopus blight, Rhizopus head rot and Rhizopus soft rot Rhizopus blight: Rhizopus blight can affect flowers, leaves, and stems. When infected, the plant shows symptoms such as soft and mushy brown rot. The rot produces white mycelia with black sporangia and the abundant mycelia projects a ‘bearded’ appearance. Spores of the fungus can be spread by water and air. The mode of infection is similar to bacterial soft rot in which enzymes secreted by the fungus causes cell deterioration of the host tissue. The fungi require high temperatures, high humidity and weakened host tissues or wounds (Hartley 1992). Rhizopus head rot on sunflowers: Rhizopus head rot may be caused by several Rhizopus species such as Rhizopus arrhizus, R. microsporus and R. stolonifer (Markell et al. 2015). Historically, Rhizopus head rot was deemed as a minor disease. However, recent surveys have shown their severity. Initial signs of Rhizopus head rot are dark spots of different sizes on different types of wounds on the plant. Soft watery rot appears on the infected fruit which often turns dark brown and extends to the back of the flower head, sepals and peduncles as the disease progresses. The infected sunflower receptacle disintegrates and becomes soft and pulpy. Infection by Rhizopus causes the head to shrivel and dry. Morphological characteristics are mycelial strands bearing sporangiophore and sporangia which are seen as the disease advances (Markell et al. 2015; Zhou et al. 2018). These whiskers are tufts of hyphae containing numerous sporangia and generally appear around lenticels or breaks in the periderm. Sometimes hyphae may not be visible on the outside of the root but can be viewed by pulling apart the infected tissue, giving it a stringy appearance (Clark et al. 2013). 13 194 Table 26 DNA barcodes available for Rhizopus Fungal Diversity (2020) 103:87–218 Species name Isolate no SSU ITS LSU Rhizopus americanus R. arrhizus# CBS 340.62* CBS 111231 CBS 544.80 NRRL 1469 CBS 427.87* 33515 CBS 392.95 CBS336.62* FSU2530 EML-HO95-1* EML-HO95-2 strain FSU10053 CBS 319.35 CBS 320.35 CBS 699.68* CBS 337.62 IFO 4810 CBS 112.07* CBS 130146 CBS 138.95 ATCC 96514* CBS 336.39* CBS 389.95 SICAUCC 19-0001 NG_062623 HM999967 JN206338 JN206337 DQ641279 NR_137056 AF115730 MH862535 HM999968 KJ408567 KU058202 KU058203 NG_057873 R. caespitosus R. delemar R. homothallicus R. koreanus R. lyococcus R. microsporus# R. niveus# R. oryzae# R. schipperae R. sexualis# R. stolonifer# NG_062622 NG_062624 KJ408537 KU058194 KU058195 KJ408545 AB250177 NG_062621 NG_064824 NG_063011 MN148534 AB100449 JN206373 HM999970 JN206362 DQ641284 NR_103595 MH865585 NR077174 DQ641323 AB113017 DQ641318 MN267051 NG_057871 DQ466604 MH874170 NG_057870 KJ408554 KU058196 KU058197 KJ408562 JN206534 MH869765 NG_056282 MH877020 HM849672 NG_059417 MH867536 MN148530 Ex-type/ex-epitype/ex-neotype/ex-lectotype strains are in bold and marked with an asterisk (*). Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with # Rhizopus soft rot: Common causative agents of Rhizopus soft rot are Rhizopus stolonifer and Rhizopus oryzae. The disease is considered as one of the most common and destructive postharvest diseases in many plants such as sweet potato (Ipomoea batatas), potato (Solanum tuberosum) and tomato (Solanum lycopersicum). The most frequent mode of infection is wounds and injuries present on the plants. Studies have also shown that the type of wounding and storage time have a significant impact on the susceptibility of infection by Rhizopus species (Scruggs and Quesada-Ocampo 2016). Earliest symptoms of infections are soft water-soaked lesions. The disease spreads across the wounded area and progresses to the extremities of the substrate. Hyphae soon develop on the rotten tissues and produce grey sporangiophores which subsequently bear sporangia (Khokhar et al. 2019). Whiskers are characteristics features of Rhizopus soft rot and have been reported in the case of soft rot on sweet potatoes (Clark et al. 2013; Scruggs and Quesada-Ocampo 2016) (Table 26). Hosts—Wide range of hosts including species of Allium, Ananas, Brassica, Cucumis, Cucurbita, Fragaria, Lycopersicon, Phaseolus, Pisum and Solanum (Farr and Rossman 2020) 13 Pathogen biology, disease cycle and epidemiology The pathogen reproduces asexually. Spores of Rhizopus species are commonly found in the air and can survive easily on crop debris, fruits, vegetables, and even on tools and equipment. Factors such as the Rhizopus species, type of fruit, stage of maturity of the plant and fruit or the storage will have a slight difference in the disease cycle. Rhizopus stolonifer, as well as the other species causing post-harvest diseases such as Rhizopus soft rot, require wound injuries, cracks or any mechanical damage for entry (Hartley 1992; Bautista-Baños et al. 2014; Scruggs and Quesada-Ocampo 2016). Infection and colonization are highly dependent on the enzymes produced by the fungi. To establish within the host, Rhizopus species produce numerous enzymes, including amylase, pectinase, and cellulase that can damage cell walls and permit host colonization (Ogundero 1988; Tang et al. 2012). This results in the softening of the host tissue; one of the symptoms of the disease (Nelson 2009; Kwon et al, 2012; Bautista-Baños et al. 2014; Feliziani and Romanazzi 2016). During initial stages of infection, Rhizopus rot appears as water-soaked areas and in the case of Rhizopus stolonifer, the rot also exudes clear leachate. In the case of Rhizopus soft rot caused by R. oryzae in banana, Fungal Diversity (2020) 103:87–218 the symptoms and disease cycle are similar to R. stolonifer (Kwon et al. 2012). In Okinawan sweet potatoes, the disease causes a soft and moist appearance and a stringy flesh during the initial stages and as the disease progresses, the tissue of the sweet potato turns brownish and eventually black (Nelson 2009). In the case of R. stolonifer, the fungal mycelia quickly spread across the infection site. The sporangia formed are normally black and the whole plant is covered by fungal mycelia (Bautista-Baños et al. 2014). The enzymes exuded from the pathogen generally liquefy the internal tissues, for an example in sweet potato parenchyma of the root becomes liquefied, leaving the periderm and outer fibres of the root intact (Scruggs and Quesada-Ocampo 2016). The disease becomes more severe in warm, humid environments (Zoffoli and Latorre 2011). Avoidance of Rhizopus species is difficult due to their ubiquitous nature; therefore, sanitation and storing produce under unfavourable disease conditions is the key to control this pathogen. Morphology- based identification and diversity Rhizopus is normally distinguished by rhizoids, stolons and single or branched sporangiophores (Vebliza et al. 2018). Identification of species takes into account the growth temperature, size of sporangiophore and sporangium and the branching of rhizoids (Abe et al. 2007). The white mycelia consist of coenocytic hyphae which bear the sporangiophore with normally black sporangia. These taxa are fast-growing and form rhizoids at the base of sporangiophores. The sporangium contains a columella and spores (Bullerman 2003). During the sexual stage, there is the formation of zygospores and chlamydospores can also be seen during the growth of the fungi (Bullerman 2003; Abe et al. 2007). Molecular identification and diversity Traditionally, Rhizopus species were classified using morphological characters such as the shape and size of the structures (chlamydospores, rhizoids, sporangiophores and columellae) and physiological features such as optimal growth conditions. Current classification and taxonomic grouping follow that of Schipper (Schipper 1984). Schipper classified Rhizopus into three groups namely R. microsporus, R. stolonifer and R. arrhizus based on the physiological factors and morphology (Abe et al. 2010; Gryganskyi et al. 2018). Later, studies such as Abe et al. (2006), Liu et al. (2007), Zheng et al. (2007a, b), Abe et al. (2010) implemented molecular phylogeny using DNA sequence data in the classification of these fungi. With novel approaches used, the classification proposed by Schipper was found to agree with some recent studies while others divided the genus into ten species and seven varieties or eight species. Zheng et al. (2007b) used zygospore formation, and molecular systematic 195 morphological characters, mating compatibility, physiology and molecular systematic to accept the division of the genus in ten species and seven varieties. Abe et al. (2010) also used the rDNA ITS gene region together with actin-1 and tef1, to reorganize the proposed taxonomy into eight species instead of ten species. One important data provided by this study was the problematic rDNA ITS region of R. americanus. It was discovered that R. sexualis var. americanus has three rDNA ITS gene regions which are distinct from each other. However, Liu et al. (2007) were not able to obtain all three rDNA ITS gene region instead they were able to amplify only one ITS region which was similar to that of Rhizopus oryzae. So, this led to the conclusion that R. americanus was phylogenetically different from R. sexualis. Genetic markers (species and genus level)—ITS and rpb1 Genetic markers (higher-level phylogeny)—SSU, LSU and act Accepted number of species—There are 152 species epithets in Index Fungorum (2020), however only 12 species have DNA sequence data (Table 25). References—Bullerman (2003), Abe et al. (2007) (morphology); Abe et al. (2010), Gryganskyi et al. (2018), Vebliza et al. (2018) (morphology and phylogeny) Discussion This is the fourth in the One Stop Shop series focusing on providing a stable platform for the taxonomy of plant pathogenic fungi and fungus-like organisms. These series aim to provide updated backbone trees and information regarding plant pathogens in one place for ease of access. Databases play an important role in aggregating the scattered data into an easily accessible form and many of the pathogenic genera were annotated in the UNITE database (Nilsson et al. 2014). However, this database mainly focused on ITS region rather than the protein-coding gene regions. There are very few databases dedicated to identity the plant pathogens and related fungi-like organisms. We have been trying to provide a stable and updated taxonomy for 97 genera and three families since 2014, which are listed in Table 1. All this information is available in http://www.onestopshopfungi.org. Acknowledgements Dr Yong Wang thanks National Natural Science Foundation of China (No. 31972222, 31560489), Program of Introducing Talents of Discipline to Universities of China (111 Program, D20023), Talent project of Guizhou Science and Technology Cooperation Platform ([2017]5788-5 and [2019]5641) and Guizhou Science, Technology Department International Cooperation Basic project ([2018]5806), Guizhou University cultivation project [2017]5788-33. Kevin D. Hyde would like to thank “the future of specialist fungi in a changing climate: baseline data for generalist and specialist fungi associated with ants, Rhododendron species and Dracaena species” 13 196 (Grant No. DBG6080013), Thailand Research Fund (TRF) Grant no RDG6130001 “Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion”. Work of Viktor Papp was supported by the Ministry for Innovation and Technology within the framework of the Higher Education Institutional Excellence Program (NKFIH-1159-6/2019) in the scope of plant breeding and plant protection research of Szent István University. Sinang Honsanan would like to thank the National Natural Science Foundation of China for supporting the Project no. 31950410548. Our thanks are due to the Research and Researchers for Industries Grant (PHD57I0015) for financial support to Boontiya Chuankid. Napalai Chaiwan would like to thank the Royal Golden Jubilee PhD Program under Thailand Research Fund (RGJ) The scholarship no. PHD60K0147. Mingkwan Doilom thanks the 5th batch of Postdoctoral Orientation Training Personnel in Yunnan Province (Grant no.: Y934283261) and the 64th batch of China Postdoctoral Science Foundation (Grant no.: Y913082271). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. 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Harischandra2,7,9 · Ajay Kumar Gautam10 · Shubhi Avasthi11 · Boontiya Chuankid2,7 · Ishani D. Goonasekara2,7 · Sinang Hongsanan12 · XiangYu Zeng2,7,19 · Kapila K. Liyanage2,17,20 · NingGuo Liu2 · Anuruddha Karunarathna2,8 · Kalani K. Hapuarachchi2 · Thatsanee Luangharn2,3 · Olivier Raspé2,7 · Rashika Brahmanage2,7,9 · Mingkwan Doilom3,16,17 · Hyang B. Lee13 · Liu Mei9 · Rajesh Jeewon14 · Naruemon Huanraluek2 · Napalai Chaiwan2,7 · Marc Stadler15 · Yong Wang1 1 Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, Guizhou, China 2 Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand 3 Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People’s Republic of China 4 Department of Botany, Szent István University, Villányi út 29-43, Budapest 1118, Hungary 5 Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 6 14456, USA 6 Department of Pomology, Szent István University, Villányi út 29-43, Budapest 1118, Hungary 7 School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand 8 9 Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, No. 9 of Shuguanghuayuanzhonglu, Chiang Mai 50200, Thailand Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Haidian DistrictHaidian District, Beijing 100097, People’s Republic of China 10 School of Agriculture, Abhilashi University, Mandi, Himachal Pradesh 175028, India 11 School of Studies in Botany, Jiwaji University, Gwalior 474011, India 13 12 Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, PR China 13 Environmental Microbiology Lab, Dept. of Agricultural Biological Chemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea 14 Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius 15 Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany 16 Honghe Innovation Center for Mountain Futures, Kunming Institute of Botany, Honghe County, Yunnan 654400, People’s Republic of China 17 World Agroforestry Centre, East and Central Asia, Kunming 650201, Yunnan, People’s Republic of China 18 Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China 19 Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand 20 Rubber Research Institute of Sri Lanka, Dartonfield, Agalawatta, Sri Lanka

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