One stop shop III: taxonomic update with molecular phylogeny for important phytopathogenic genera: 51–75 (2019)

Ruvishika S Jayawardena

A total of eight species of Alternaria denoted by nine isolates were collected from diverse crops and variation among them was examined by protein profiling and RAPD-PCR techniques. Most of the isolates amplified similar bands of DNA which were used as measures of the degree of resemblance among isolates. The phylogenetically linked out group genus Stemphylium could not be clearly separated using RAPD analysis. No correlation was found between RAPD cluster analysis and pathogenic abilities of the isolates tested.

Alternaria is a plant pathogenic fungus with a wide host range and causes disease in different types of plant. In the present study, eleven Alternaria isolates were collected from infected samples of different host plant belonging to diverse families. Identification and study of diversity study was done based on the morphological features of the isolates i.e., colony characteristics size, septation and beak length of conidia. Genetical variability among the isolates was carried out by using three RAPD primers. All isolates were identified as belonging to the genus Alternaria. The diversity analysis showed that seven of the isolates were different from each. However, TD7 and TD2 resembled in their morphological as well as genetical characters, similarly TD17 and TD12 were also found similar. No significant relationship could be established between host plant infected and pathogen morphological or genetics. It was however apparent that Alternaria sp. may be morphologically similar but...

Alternaria is a ubiquitous fungal genus which includes endophitic, saprophytic and pathogenic species. They can cause pre and post-harvest diseases in numerous crops and world-wide economic losses. Alternaria spp. with small conidia size, less than 60 μm, are categorized as small spore Alternaria. Alternaria alternata, Alternaria arborescens, and Alternaria tenuissima are among the most commonly reported small spore Alternaria spp. These species represent a disease complex on some hosts, often isolated from a single plant. Among the species, there remain overlapping morphological characteristics, and often it is not easy to differentiate the species microscopically. These pathogens usually appeared in anamorph, or asexual reproductive stage and the sexual reproduction is mostly known. There are very few studies on the genetic structure and evolutionary trajectory of the pathogen populations in the agroecosystems. The conidia are usually produced on leaf lesions, and often colonize i...

Fungal Diversity https://doi.org/10.1007/s13225-019-00433-6 (0123456789().,-volV)(0123456789(). ,- volV) One stop shop III: taxonomic update with molecular phylogeny for important phytopathogenic genera: 51–75 (2019) Ruvishika S. Jayawardena1,2 • Kevin D. Hyde1,2,3 • Eric H. C. McKenzie4 • Rajesh Jeewon5 • Alan J. L. Phillips6 • Rekhani H. Perera2,7 • Nimali I. de Silva2,8 • Sajeewa S. N. Maharachchikumburua9 Milan C. Samarakoon2,8 • Anusha H. Ekanayake2 • Danushka S. Tennakoon2,7 • Asha J. Dissanayake2 • Chada Norphanphoun2,7 • Chuangen Lin2,7 • Ishara S. Manawasinghe2,7,10 • Qian Tian2,7 • Rashika Brahmanage2,7,10 • Putarak Chomnunti2,7 • Sinang Hongsanan11 • Subashini C. Jayasiri2,7 • F. Halleen12,13 • Chitrabhanu S. Bhunjun2,7 • Anuruddha Karunarathna2,8 • Yong Wang1 • Received: 3 June 2019 / Accepted: 23 July 2019 Ó School of Science 2019 Abstract This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and organisms. This paper focuses on 25 phytopathogenic genera: Alternaria, Capnodium, Chaetothyrina, Cytospora, Cyphellophora, Cyttaria, Dactylonectria, Diplodia, Dothiorella, Entoleuca, Eutiarosporella, Fusarium, Ilyonectria, Lasiodiplodia, Macrophomina, Medeolaria, Neonectria, Neopestalotiopsis, Pestalotiopsis, Plasmopara, Pseudopestalotiopsis, Rosellinia, Sphaeropsis, Stagonosporopsis and Verticillium. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. A new database (Onestopshopfungi) is established to enhance the current understanding of plant pathogenic genera among plant pathologists. Keywords Classification Database Plant pathology Phylogeny Taxonomy Symptoms Systematics & Yong Wang yongwangbis@aliyun.com 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 8 Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand 9 School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, People’s Republic of China 10 Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, No. 9 of Shuguanghuayuanzhonglu, Haidian District, Beijing 100097, People’s Republic of China 11 College of Life Science and Oceanography, Shenzhen University, 1068, Nanhai Avenue, Nanshan, Shenzhen 518055, China 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 Landcare Research-Manaaki Whenua, Private Bag 92170, Auckland, New Zealand 5 Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius 12 Plant Protection Division, ARC Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch 7599, South Africa 6 Faculdade de Ciéncias, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal 13 Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa 7 School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand 123 Fungal Diversity Contents and contributors (main contributors underlined) 51. Capnodium–P Chomnunti, RS Jayawardena 52. Chaetothyrina–S Hongsanan, RS Jayawardena 53. Cytospora–C Norphanphoun, RS Jayawardena, KD Hyde 54. Cyphellophora–Q Tian, RS Jayawardena 55. Cyttaria–AH Ekanayake 56. Dactylonectria–RH Perera 57. Entoleuca–MC Samarakoon 58. Eutiarosporella–RS Brahmanage, AJL Phillips, RS Jayawardena 59. Ilyonectria–RH Perera 60. Macrophomina–DS Tennakoon, AJL Phillips 61. Medeolaria–AH Ekanayake 62. Neonectria–RH Perera, F. Halleen 63. Neopestalotiopsis–NI de Silva, SSN Maharachchikumbura, RS Jayawardena 64. Plasmopara–IS Manawasinghe, EHC McKenzie 65. Pseudopestalotiopsis–NI de Silva, SSN Maharachchikumbura, RS Jayawardena 66. Rosellinia–MC Samarakoon 67. Sphaeropsis–DS Tennakoon, AJL Phillips Updated genera 68. Alternaria–RS Jayawardena, KD Hyde 69. Diplodia–AJ Dissanayake, AJL Phillips 70. Dothiorella–RS Jayawardena, AJL Philips 71. Fusarium–RH Perera 72. Lasiodiplodia–AJL Phillips, RS Jayawardena 73. Pestalotiopsis–NI de Silva, SSN Maharachchikumbura 74. Stagonosporopsis–SC Jayasiri, RS Jayawardena 75. Verticillium–CG Lin Introduction One stop shop (OSS) is a series of papers focused on providing a stable platform for the taxonomy of plant pathogenic fungi and organisms. Genera included in these paper series are associated with plant diseases. However, some may not be well-known plant pathogens and Kochs’ postulates might have not been conducted in order to establish their pathogenicity. When this series was launched in 2014, its specific aims were mentioned (Hyde et al. 2014). Two issues of OSS have been published in which 50 genera were treated (Hyde et al. 2014; Jayawardena et al. 2019). In this study we treat 25 genera of plant pathogens as well as establish a new website, www.onestopshopfungi. org, to host a database for plant pathogenic fungi and 123 organisms. This fungal database allows mycologists and plant pathologists to understand disease symptoms, host distribution, classification, morphology and provides an updated phylogeny which will enhance current understanding of plant pathogens and gain better insights into the current fungal classification system. The Onestopshopfungi webpage is an output funded by the Mushroom Research Foundation, Thailand, which is a non-government and nonprofit organization. We invite all mycologists to contribute to make this a success. The outcome of this series provides a stable taxonomy and phylogeny for plant pathogens that can provide a reliable platform for mycologists and plant pathologists to accurately identify causal organisms. Material and methods Photo plates of the symptoms of the disease and morphological characters are given, when available. Classification follows Wijayawardene et al. (2018). Sequence data from ex-type, ex-epitype or authentic strains for each species were retrieved from GenBank. Sequence data from single gene regions were aligned using Clustal X1.81 (Thompson et al. 1997) and further alignment of the sequences were carried out by 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 for each genus. Phylogenetic analyses consisted of maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (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 2012) or RAxML-HPC2 on XSEDE (8.2.8) in the CIPRES science gateway platform (Miller et al. 2010) using GTR?I?G model of evolution. Bayesian inference was used to construct the phylogenies using Mr. Bayes v.3.1.2 (Ronquist and Huelsenbeck 2003). MrModeltest v. 2.3 (Nylander et al. 2008) was used for statistical selection of best-fit model of nucleotide substitution and was incorporated into the analyses. Results Capnodium Mont., Annls Sci. Nat., Bot, sér. 3, 11: 233 (1849) Fungal Diversity The genus Capnodium was introduced by Montagne (1849) to accommodate C. salicinum. Capnodium is one of the most commonly found sooty moulds in gardens and landscapes (Laemmlen 2011). Capnodium has a saprobic association with sap-feeding insects in the Order Homoptera, which includes aphids, whiteflies, soft scale, mealy bugs, leafhoppers and psyllids (Barr 1987). Gavrilov-Zimin (2017) reported that the larvae and female of a new species and a new monotypic genus of legless mealybug, Orbuspedum machinator, from bamboo twigs in southern Thailand are covered with densely packed fungal hyphae of the sooty mould Capnodium sp. Herath et al. (2012) reported that a tropical sooty mould (Capnodium sp.) is known to produce antibiotics such as tetramic acid, methiosetin and epicorazin A. Capnodium species grow on honeydew, gradually covering the surface of the plant part affected by insects, colouring it with various shades of black. These fungi do not colonize the plant tissues or trigger symptoms. However, they alter the ability of the plant to perform photosynthesis and exchange of gases with the atmosphere. Severely affected leaves may die and fall, thereby affecting plant growth and survival. Therefore, we treat Capnodium as a main plant pathogenic group. Classification—Dothideomycetes, Dothideomycetidae, Capnodiales, Capnodiaceae Type species—Capnodium salicinum Mont., Annls Sci. Nat., Bot, sér. 3 11:234 (1849) Distribution—Species of Capnodium have a wide distribution but are most common in tropical and subtropical regions (Chomnunti et al. 2014). They can be found on plants that have been previously fed upon by insects. Disease symptoms—Dark mycelium coating surface of host can cause chlorosis and reduce photosynthetic ability of plants, which effects plant growth, reduces yield, and leading to marketability problems (Chomnunti et al. 2014; Fig 1). In higher latitudes, Capnodium spp. are scarce during the winter; the most common being C. salicinum in the UK (Cannon et al. 1985; Royal Botanic Gardens, Kew, UK National Collection of Dried Fungi, unpublished data). Warm-temperate climates in Australia and the Mediterranean countries provide an abundance of perennial foliage on which sooty moulds are able to establish themselves during the winter, and so persist from one season to the next (Fraser 1935; Reynolds and Gilbert 2005). In northern Thailand, most of the sooty mould infections are caused by Capnodium species (Chomnunti et al. 2014). Hosts—Many plants when colonised by insects that produce honeydew. Species of Annona, Camellia, Citrus, Coffea, Chrysophyllum, Ficus, Malus, Mangifera, Olea, Populus, Prunus, Psidium, Rhododendron and Salix (Farr and Rossman 2019) Morphological based identification and diversity The asexual morph forms elongated pycnidia that develop from a superficial mycelium on living plant surfaces and produce tiny, hyaline conidia on top of the pycnidia (Chomnunti et al. 2011). Persoon (1822) mention that Fumago citri is the sooty mould but it was not well described and completed; therefore it was transferred to genus Polychaeton by Léveillé (1847). Later, Berkeley- Fig. 1 Sooty moulds on various host plants associated with insects. a On a hardwood tree, b on guava, c on coffee, d–f on mango 123 Fungal Diversity Desmazieres (1849) transferred all species once known in the genus Fumago to Capnodium. Molecular evidence revealed that Polychaeton is an asexual stage of Capnodium, therefore, both are the same organism. According to ‘‘one fungus one name’’ and the Melbourne Code under Art. 57.2, Capnodium was considered for conservation as it has a larger number of epithets and is more widely used in this group of fungi, even though Polychaeton is the older name (Chomnunti et al 2011, 2014; McNeill et al. 2012; Hyde et al. 2013; Wijayawardene et al. 2014, 2017, 2018; Liu et al. 2015; Hongsanan et al. 2015). The morphology of Capnodium species can be recognised by black mycelial growth spreading on the host surface, which produces superficial colonies with septate, dark brown hyphae and cylindrical and bitunicate asci. On host surface Capnodium species share the same ecological niche and are similar in appearance to other genera and families of sooty moulds; often found with sexual and asexual states growing together and living in complex communities (Faull et al. 2002; Hughes 2003; Hughes and Seifert 2012; Chomnunti et al. 2014; Hongsanan et al. 2015). Table 1 Details of Capnodium isolates used in the phylogenetic analyses Species Isolate/voucher no ITS C. coffeae AFTOL-ID 939 DQ491515 C. coffeae CBS 147.52 AJ244239 Capnodium coffeae CTQE057 KX893384 Capnodium coffeicola MFLUCC 15-0206* KU358921 Capnodium salicinum CBS 131.34 AJ244240 Capnodium sp. SZ-F22 KT443921 Capnodium sp. Capnodium sp. S80 CP1 MH633887 MH629975 Capnodium sp. OUCMBI101100 HQ914834 Capnodium sp. ELM115 KU556052 Capnodium sp. GPO-CO-02 KC180729 Capnodium sp. agrFF1633 HE584839 Capnodium sp. agrFF1683 HE584838 Capnodium sp. agrFF1681 HE584837 Capnodium sp. agrFF1679 HE584836 Capnodium sp. agrFF1678 HE584835 Capnodium sp. agrFF1639 HE584834 Capnodium sp. agrFF1638 HE584833 Molecular based identification and diversity Capnodium sp. agrFF1614 HE584832 Capnodium sp. agrFF1613 HE584831 DNA sequencing data of Capnodium coffeae, C. coartatum, C. salicinum, C. coffeicola and C. dematum and eleven unidentified Capnodium spp. are available in GenBank, including sequence data for LSU, SSU and ITS (4/7/2019). Hongsanan et al. (2015) introduced a new species Capnodium coffeicola. It differs from other Capnodium species in having pycnidia with short and black stalks at the base and is swollen at the central part, and it has cylindrical to oblong conidia, but its placement is supported with phylogenetic analysis using LSU and ITS sequence data. Sooty moulds often grow in colonies of more than one species, and taxonomic descriptions thus often unknowingly combine elements of different genera and species. Identification based on morphology only is difficult as there are overlapping morphological characters among many taxa (Chomnunti et al. 2011, 2014). To achieve accurate generic and species identification and taxonomic placements, phylogenetic studies using large subunit ribosomal RNA (LSU rRNA) gene sequences and the internal transcribed spacer regions and 5.8S nrDNA gene (ITS) were performed (Crous et al. 2009; Chomnunti et al. 2011, 2014; Liu et al. 2015; Hongsanan et al. 2015). This study reconstructs the phylogeny of Capnodium based on analyses of ITS sequence data (Table 1, Fig. 2) and corresponds with previous studies (Chomnunti et al. 2011, 2014; Hongsanan et al. 2015). This can be used as a backbone tree in the identification of Capnodium species (Fig. 3). Capnodium sp. agrFF0153 HE584830 Capnodium sp. Capnodium sp. agrFF1634 agrFF1631 HE584829 HE584828 Capnodium sp. agrFF0180 HE584822 Capnodium sp. agrFF1690 HE584823 Species Isolate/Voucher no ITS Capnodium sp. agrFF0045 HE584825 Capnodium sp. agrFF0207 HE584826 Capnodium sp. TMS-2011 HQ631045 Capnodium sp. TTI-247 KU985278 Conidiocarpus plumeriae MFLUCC 15-0205 KU358919 Conidiocarpus siamensis MFLUCC 10-0053 KU358922 Co. siamensis MFLUCC 10-0061 KU358923 Co. siamensis MFLUCC 10-0062 KU358924 Co. siamensis MFLUCC 10-0063 KU358925 Co. siamensis MFLUCC 10-0064 KU358926 Co. siamensis MFLUCC 10-0065 KU358927 Co. siamensis Scoria leucadendri MFLUCC 10-0074 CBS 131318 KU358928 JQ044437 123 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold Recommended genetic marker (genus level)—LSU Recommended genetic markers (species level)—LSU, ITS Sequence data of LSU, SSU and ITS are available for five species of Capnodium in GenBank but none of them has complete sequence data. LSU is useful for preliminary Fungal Diversity Fig. 2 Morphology of Capnodium sp. a pycnidia on the host. b, d, e, f stalked pycnidia c mycelium network, g conical pycnidium and pycnidial wall, h ostiole surrounded by hyaline hyphae, i conidia. Scale bars: b, d–f = 100 lm, c, g = 50 lm, h, = 20 lm, i = 10 lm identification at the generic level (Chomnunti et al 2011, 2014; Quaedvlieg et al 2014). Hongsanan et al. (2015) recommended the use of combined LSU and ITS sequence data to identify the species. More protein-coding gene loci should be sequenced to clarify the taxonomic problems in this genus. In the current analyses, C. cortatum was not included due to lack of ITS sequences in GenBank. A revision of this genus is needed as it may reveal many new species. Re-sequencing of species as well as designating epitypes or representative species is also important. Accepted number of species: There are 140 epithets in Index Fungorum (2019), however only four species have DNA sequence data. 123 Fungal Diversity Fig. 3 Phylogenetic tree generated by maximum likelihood analysis of ITS sequence data of Capnodium species. Related sequences were obtained from GenBank. Thirty-eight strains are included in the analyses, which comprise 512 characters including gaps. The tree was rooted with Scoria leucadendri (CBS 131318). Tree topology of the ML analysis was similar to the MP analysis. The best scoring RAxML tree with a final likelihood value of - 2398.970137 is presented. The matrix had 236 distinct alignment patterns, with 16.01% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.285338, C = 0.285338, G = 0.241464, T = 0.238894; 123 substitution rates AC = 1.204962, AG = 1.857184, AT = 2.642904, CG = 1.319860, CT = 4.051266, GT = 1.000000; gamma distribution shape parameter a = 0.287147. The maximum parsimonious dataset consisted of constant 327, 125 parsimony-informative and 60 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of two equally most parsimonious trees with a length of 358 steps (CI = 0.735, RI = 0.875, RC = 0.630, HI = 0.265) in the first tree. RAxML and maximum parsimony bootstrap support value C 50% are shown, respectively, near the nodes. Ex-type strains are in bold Fungal Diversity References: Chomnunti et al 2011, 2014; Quaedvlieg et al 2014; Hongsanan et al. 2015 (morphology, phylogeny). Chaetothyrina Theiss., Annls mycol. 11(6):495 (1913) The genus Chaetothyrina was established by Theissen (1913), with C. musarum (Speg.) Theiss as the type species. Chaetothyrina was placed in Micropeltidaceae based on its superficial, flattened base, poorly developed thyriothecium and irregular meandering arrangement of compact hyphae of walled cells. Singtripop et al. (2016) provided molecular data of one reference specimen and one new species. Hongsanan et al. (2017) established a new species of Chaetothyrina and introduced a new family Phaeothecoidiellaceae to accommodate species of Chaetothyrina, Houjia and Phaeothecoidiella in Capnodiales. Based on its placement in phylogenetic trees and the morphological uniqueness, Micropeltidaceae was excluded from Microthyriales and treated as family incertae sedis in Lecanoromycetes (Hongsanan et al. 2017; Zeng et al. 2019) (Fig. 4). Classification—Dothideomycetes, incertae sedis, Capnodiales, Phaeothecoidiellaceae Type species—Chaetothyrina musarum (Speg.) Theiss., Annls mycol. 11(6):495 (1913) Distribution—Known from Brazil, Cook Islands, Dominican Republic, India, Mexico, Pakistan, Panama, Thailand, US Disease symptoms—Sooty blotch and flyspeck Species in this genus cause flyspeck disease on various plants, such as C. musarum on Musa sp. and C. panamensis (F. Stevens & Dorman) Arx on Oncoba laurina. Sooty blotch and flyspeck (SBFS) is a disease complex caused by nearly 80 fungal species (Singtripop et al. 2016) that are epiphytes which blemish the epicuticular wax layer of several fruit crops, such as apple, pear, orange, persimmon, banana and grape worldwide (Gleason et al. 2011; Gao et al. 2014), cutting sale price and limiting the growth rate of fruit production (Williamson and Sutton 2000; Gao et al. 2014). ‘Sooty blotch’ is characterized by colonies produced on host tissues from superficial, spreading, dark irregular blotches of mycelium with or without sclerotium-like structures or fruiting bodies. On the other hand, ‘flyspeck’ defines clusters of shiny, small, black sclerotium-like structures or fruiting bodies, lacking visible intercalary mycelium (Gleason et al. 2011; Mayfield et al. 2012; Singtripop et al. 2016). Hosts—Species of Anacardium, Anodendron, Anogeissus, Carallia, Cassia, Chonemorpha, Dalbergia, Dianella, Euonymus, Hevea, Iiana, Magnifera, Magnolia, Mammea, Maytenus, Memecylon, Mitragyna, Musa, Myrcia, Ochrocarpos, Olea, Oncoba, Phoebe, Similax, Streblus and Vochysia. Morphological based identification and diversity Chaetothyrina is characterized by superficial, flattened thyriothecia, with base poorly developed, with thyriothecial setae and 1-septate ascospores (Reynolds and Gilbert 2005; Singtripop et al. 2016; Hongsanan et al. 2017). Chaetothyrina can be distinguished from other species in Micropeltidaceae on the basis of thyriothecial setae appearance, shape and septation of the ascospores (Singtripop et al. 2016; Hongsanan et al. 2017). Twenty-three species of Chaetothyrina epithets are listed in Index Fungorum (2019), but sequence data are available for only two species (4/7/2019). Chaetothyrina is a poorly studied genus. Fresh collections and sequence data are needed for this genus. The disease cycle of this genus is yet to be established (Fig. 5). Fig. 4 Disease symptoms caused by Chaetothyrina spp. a on mango, b, d appearance of thyriothecia on hosts, c on a banana, e on mango leaves 123 Fungal Diversity Molecular based identification and diversity Singtripop et al. (2016) provided a reference type specimen of C. musarum with sequence data. Using combined LSU, SSU and ITS sequence data, Chaetothyrina clustered as a sister genus to Houjia and Phaeothecoidiella within Capnodiales (Hongsanan et al. 2017; Table 2, Fig. 6). Fig. 5 Chaetothyrina guttulata a Thyriothecium when viewed in squash mount. b Surface of thyriothecium. c Section through thyriothecium. d Ascus when immature. e Asci at maturity. f Ascospores. Scale bars: a = 50 lm, b, d, e = 10 lm, c = 100 lm, f = 5 lm 123 Fungal Diversity Recommended genetic markers (genus level)—LSU and SSU Recommended genetic markers (species level)—ITS and RPB2 Accepted number of species: There are 23 epithets in Index Fungorum (2019). However, only two species have molecular data. Table 2 Details of Chaetothyrina isolates used in the phylogenetic analyses References: Reynolds and Gilbert 2005; Singtripop et al. 2016; Hongsanan et al. 2017 (morphology, phylogeny) Cytospora Ehrenb., Sylv. mycol. berol.: 28 (1818) Cytospora was introduced by Ehrenberg (1818) as the type genus of the family Cytosporaceae in Diaporthales (Wehmeyer 1975; Barr 1978; Eriksson et al. 2001; Castlebury et al. 2002). The genus is an important Species Isolate/voucher no LSU SSU ITS Austroafricana associata CBS 120732 KF901829 – KF901512 Capnobotryella renispora CBS 215.90 GU214399 AY220613 AY220613 Capnodium coffeae CBS 147.52 GU214400 DQ247808 AJ244239 Chaetothyrina guttulata MFLUCC15-1080 KU358917 KU358916 KX372277 C. guttulata MFLUCC15-1081* KU358914 KU358915 KX372276 C. musarum MFLUCC15-0383 KU710171 KU710174 KX372275 C. musarum MFLUCC15-0383 KU710171 KU710174 KX372275 Devriesia strelitziae CBS 122379 GU301810 GU296146 EU436763 Dissoconium aciculare CBS 204.89 GU214419 GU214523 AY725520 D. dekkeri CBS 342.86 JN232431 – – Dothistroma septosporum CBS:112498 GQ852597 JX901744 JX901744 Hortaea werneckii 4263 JX141471 JX141470 DQ336709 Houjia yanglingensis YHLB20 GQ433630 – GQ433629 H. yanglingensis YHJN13* GQ433631 – GQ433628 Leptoxyphium cacuminum Mycosphaerella ellipsoidea MFLUCC10-0049* CBS:110843* JN832602 GQ852602 JN832587 AY725545 AY725545 M. endophytica CBS:114662* GQ852603 DQ302953 DQ302953 – M. keniensis CBS:111001* GQ852610 – Myriangium duriaei CBS 260.36 NG027579 AF242266 – M. hispanicum CBS 247.33 GU301854 GU296180 – Phaeothecoidiella illinoisensis CBS:125223 GU117901 – GU117897 P. missouriensis CBS:118959 GU117903 – GU117899 Phragmocapnias asiticus MFLUCC10-0062 JN832612 JN832597 – P. betle MFLUCC10-0053 JN832606 JN832591 – P. betle MFLUCC10-0050 JN832605 JN832590 – Pseudoveronaea ellipsoidea MI3 34F1a* JQ622103 – FJ425205 P. obclavata UIF3 AY598916 – AY598877 Ramichloridium apiculatum CBS 400.76 EU041851 EU041794 EU041794 Rasutoria pseudotsugae rapssd EF114704 EF114729 EF114687 R. tsugae ratstk EF114705 EF114730 EF114688 Schizothyrium pomi S. pomi CUA1a Flyspeck1924-Zj001 AY598895 AY598894 – – EF164898 AY598848 Scorias spongiosa MFLUCC10-0084 JN832586 JN832601 – S. spongiosa AFTOL-ID 1594 DQ678075 DQ678024 – Stomiopeltis versicolor GA3 23C2b FJ147163 – FJ438375 Zygophiala cryptogama KY1 1.2A1c* EF164902 – EF164900 Z. tardicrescens MWA1a* EF164901 – AY598856 Z. wisconsinensis MSTA8a* AY598897 – AY598853 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold 123 Fungal Diversity Fig. 6 Phylogenetic tree generated by maximum parsimony analysis of combined LSU, SSU and ITS sequence data. Thirty-nine strains are included in the analyses, which comprised 2225 characters including gaps. The tree was rooted with Myriangium duriaei (CBS 260.36) and M. hispanicum (CBS 247.33). The maximum parsimonious dataset consisted of 1645 constant, 461 parsimony-informative and 119 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 = 0.549, RI 0.736, RC = 0.404, HI = 0.451) in the first tree. MP and ML bootstrap values C 50% and bayesian posterior probabilities C 0.90 (BYPP) are shown respectively near the nodes. Ex-type strains are in bold pathogenic fungus, causing canker and dieback on branches of a wide range of hosts with a wide distribution (Adams et al. 2005, 2006; Hyde et al. 2017, 2018; Norphanphoun et al. 2017, 2018). Classification—Sordariomycetes, Diaporthomycetidae, Diaporthales, Valsaceae Type species—Cytospora chrysosperma (Pers.) Fr. 1823 Distribution—Worldwide Disease symptoms—Canker and dieback disease on branches Hosts—Species of Abies, Acer, Berberis, Betula, Ceratonia, Cornus, Cotinus, Crataegus, Elaeagnus, Eriobotrya, Eucalyptus, Juniperus, Lumnitzera, Malus, Picea, Pinus, Platanus, Platycladus, Populus, Prunus, Pyrus, Quercus, Rosa, Salix, Sequoia, Sibiraea, Sorbaronia, Sorbus, 123 Fungal Diversity Spiraea, Styphnolobium, Syringa, Syzygium, Tibouchina, Ulmus, Vitis and Xylocarpus (Norphanphoun et al. 2018). Morphological based identification and diversity Cytospora is characterized by multi-loculate conidiomata with ostiolar necks and unicellular, elongate-allantoid to subcylindrical, hyaline conidia (Fan et al. 2015a, b; Norphanphoun et al. 2017, 2018; Fig. 7). The genus which was reported as causing canker diseases in many woody plants was established in 1818 and studied in detail by taxonomists (Fries 1823; Saccardo 1884). Valsa Fr. was reported as the sexual stage of this genus and therefore, Valsa was treated as a synonym of Cytospora (1818) based on The International Code of Nomenclature for Algae, Fungi, and Plants (ICN, McNeill et al. 2012), with Cytospora being the oldest and most widely used name (Adams et al. 2005; Fotouhifar et al. 2010; Fan et al. 2014; Rossman et al. 2015). Previously, the conventional identification of species in Cytospora was based on their host association, often with vague morphological descriptions. Mycologists began to elucidate the relationships between Cytospora species and their hosts, with morphological observations combined with phylogenetic analyses using internal transcribed spacer (ITS) regions as an effective fungal DNA barcode (Adams et al. 2005, 2006; Fotouhifar et al. 2010; Schoch et al. 2012). The establishment of multi-gene analyses using ITS, LSU, ACT, RPB2, TUB2 has proved comprehensive for the species level (Fan et al. 2015a, b, 2020; Liu et al. 2015; Yang et al. 2015; Hyde et al. 2016; Li et al. 2016; Norphanphoun et al. 2017, 2018; Phookamsak et al. 2019). Molecular based identification and diversity Comprehensive multigene phylogenetic analyses for this genus were performed by Fan et al. (2015a, b, 2020) and Norphanphoun et al. (2017, 2018). This study reconstructs the phylogeny of Cytospora based on analyses of a combined ITS, LSU, ACT and RPB2 sequence data (Table 3, Fig 8). The phylogenetic tree is updated with recently introduced Cytospora species and corresponds to previous studies (Norphanphoun et al. 2018). Recommended genetic markers (genus level)—LSU, ITS Recommended genetic markers (species level)—ITS, ACT and RPB2 Accepted number of species: There are 630 species in Index Fungorum (2019) and 110 species have molecular data. References: Fan et al. 2015a, b, Lawrence et al. 2016, Senanayake et al. 2017, 2018 (morphology), Norphanphoun et al. 2017, 2018 (morphology, phylogeny). Cyphellophora G.A. de Vries, Mycopath. Mycol. appl. 16(1):47(1962) Cyphellophora is cosmopolitan, comprising species distributed from a broad range of environmental sources as human and animal disease, saprobes, epiphytes and plant pathogens (de Hoog et al. 1999, 2000; Jacob and Bhat 2000; Decock et al. 2003; Crous et al. 2007; Zhuang et al. 2010; Feng et al. 2014; Mayfield et al. 2012; Gao et al. 2014; Phookamsak et al. 2019). Most species, including the type species, C. laciniata, were isolated from nails or skin of humans, resulting in clinical symptoms (Feng et al. 2014). Phylogenetically, C. phyllostachysdis clustered with C. europaea, a human or mammal infection of hyperkeratosis (de Hoog et al. 2000). In contrast, C. phyllostachysdis causes sooty blotch and flyspeck (SBFS) of bamboo and is not found on humans (Gao et al. 2014). The sooty mould species C. jingdongensis was introduced with a sexual morph; it reduces plant photosynthesis but does not damage or cause disease of the plant (Chomnunti et al. 2014; Yang et al. 2018). Classification—Eurotiomycetes, Chaetothyriomycetidae, Chaetothyriales, Cyphellophoraceae Type species—Cyphellophora laciniata G.A. de Vries, Mycopath. Mycol. appl. 16(1):47(1962) Distribution—Australia, Brazil, China, Germany, India, Israel, Korea, Taiwan Disease symptoms—Sooty blotch and flyspeck (main symptoms of this disease are given under Chaetothyrina). To date, C. artocarpi, C. guyanensis, C. jingdongensis, C. musae, C. olivacea, C. oxyspora, C. phyllostachydis and C. sessilis have been isolated from plant materials (Gams and Holubová-Jechová 1976; de Hoog et al. 1999; Decock et al. 2003; Gao et al. 2014; Yang et al. 2018). Cyphellophora artocarpi, C. musae, C. phyllostachydis and C. sessilis were reported to cause sooty blotch and flyspeck from apple, jackfruit (Artocarpus heterophyllus) and bamboo (Phyllostachys heterocycla, Sinobambusa tootsik), resulting in significant economic damage (Zhuang et al. 2010; Mayfield et al. 2012; Gao et al. 2014). Hosts—Artocarpus heterophyllus, Dendrocalamus strictus, Eucalyptus sp., Helomeco velane, Hylomecon verlance, Malus domestica, Musa sp., Phyllostachys sp., Sinobasmbusa tootsik and Stenocalyx uniflorus. Morphological based identification and diversity It is difficult to identify this black yeast-like genus based solely on morphological characters since the characters are very similar to those of other black yeast-like fungi, such as Phialophora and Pseudomicrodochium. Species of Cyphellophora resemble those of Phialophora in having melanized thalli with intercalary or terminal phialides bearing collarettes, but Phialophora has aseptate conidia whereas Cyphellophora produces larger, fusiform to 123 Fungal Diversity Fig. 7 Cytospora ampulliformis a stromatal habit in wood. b fruiting bodies on the substrate. c Surface of fruiting bodies. d Cross-section of the stroma showing conidiomata. e Peridium, f ostiolar neck. g–i Conidiogenous cells with attached conidia. j Mature conidia. k, l Colonies on MEA (k-from above, l-from below). Scale bars: a = 2 mm, b = 1 mm, c = 500 lm, d, f = 200 lm, e = 50 lm, g, h = 10 lm, i, j = 5 lm sigmoid, aseptate to multi-septate conidia (Réblová et al. 2013). Cyphellophora can also be compared to Pseudomicrodochium, the former having melanized thalli while they are hyaline in Pseudomicrodochium (Decock et al. 2003; de Hoog et al. 2000, 2011). Yang et al. (2018) introduced C. jingdongensis as the first sexual morph, which is characterized by subglobose to globose, non-ostiolate ascomata, ellipsoidal to cylindrical asci and fusoid, 1–3 septate ascospores. However, the asexual morph of C. jingdongensis was difficult to observe in culture to 123 Fungal Diversity Table 3 Details of Cytospora isolates used in the phylogenetic analyses Species Isolate no GenBank accession numbers ITS LSU ACT RPB2 tef1 TUB2 Cytospora acacia CBS 468.69 DQ243804 – – – – – C. ailanthicola CFCC 89970* MH933618 MH933653 MH933526 MH933592 MH933494 MH933565 C. abyssinica CMW 10181* AY347353 – – – – – C. ampulliformis MFLUCC 16-0583* KY417726 KY417760 KY417692 KY417794 – – C. amygdali CBS 144233* MG971853 – MG972002 – – – C. atrocirrhata CFCC 89615 KR045618 KR045700 KF498673 KU710946 KP310858 KR045659 C. austromontana C. beilinensis CMW 6735* CFCC 50493* AY347361 MH933619 – MH933654 – MH933527 – – – MH933495 – MH933561 C. berberidis CFCC 89927* KR045620 KR045702 KU710990 KU710948 KU710913 KR045661 C. berkeleyi StanfordT3* AY347350 – – – – – C. brevispora CBS 116811* AF192315 – – – – – C. bungeanae CFCC 50495* MH933621 MH933656 MH933529 MH933593 MH933497 MH933563 C. californica CBS 144234* MG971935 - MG972083 – MG971645 – C. carbonacea CFCC 89947 MH933622 MH933657 MH933530 MH933594 MH933498 MH933564 C. carpobroti CMW 48981* MH382812 MH411216 – – MH411212 MH411207 C. cedri CBS 196.50 AF192311 – – – – – C. celtidicola CFCC 50497* MH933623 MH933658 MH933531 MH933595 MH933499 MH933566 C. centravillosa MFLUCC 16-1206* MF190122 MF190068 – MF377600 – – C. ceratosperma CBS 116.21 AY347335 – – – – – C. ceratospermopsis CFCC 89626* KR045647 KR045726 KU711011 KU710978 KU710934 KR045688 C. chrysosperma CFCC 89981 MH933625 MH933660 MH933533 MH933597 MH933501 MH933568 C. cinereostroma C. cotini CMW 5700* MFLUCC 14-1050* AY347377 KX430142 – KX430143 – – – KX430144 – – – – C. curvata MFLUCC 15-0865* KY417728 KY417762 KY417694 KY417796 – – C. davidiana CXY 1350* KM034870 – – – – – C. diatrypelloidea CMW 8549* AY347368 – – – – – C. elaeagni CFCC 89632 KR045626 KR045706 KU710995 KF765708 KU710918 KR045667 C. eriobotryae IMI 136523* AY347327 – – – – – C. erumpens MFLUCC 16-0580* KY417733 KY417767 KY417699 KY417801 – – C. eucalypti LSEQ AY347340 – – – – – C. eucalypticola ATCC 96150* AY347358 – – – – – C. eucalyptina CMW 5882 AY347375 – – – – – C. eugeniae CMW 7029 AY347364 – – – – – C. euonymicola CFCC 50499* MH933628 MH933662 MH933535 MH933598 MH933503 MH933570 C. euonymina CFCC 89993* MH933630 MH933664 MH933537 MH933600 MH933505 MH933590 C. fraxinigena MFLUCC 14-0868* MF190133 MF190078 – – – – C. friesii CBS 194.42 AY347328 – – – – – C. fugax C. germanica CBS 203.42 CXY 1322 AY347323 JQ086563 – JX524617 – – – – – – – – C. gigalocus CFCC 89620* KR045628 KR045708 KU710997 KU710957 KU710920 KR045669 MG971664 C. granati CBS 144237* MG971799 – MG971949 – MG971514 C. hippophaës CFCC 89639 KR045632 KR045712 KU711001 KU710961 KU710924 KR045673 C. japonica CBS 375.29 AF191185 – – – – – C. joaquinensis CBS 144235* MG971895 – MG972044 – MG971605 MG971761 C. junipericola MFLU 17-0882* MF190125 MF190072 – – MF377580 – C. juniperina CFCC 50501* MH933632 MH933666 MH933539 MH933602 MH933507 – C. kantschavelii CXY 1383 KM034867 – – – – – 123 Fungal Diversity Table 3 (continued) Species Isolate no GenBank accession numbers ITS LSU ACT RPB2 tef1 TUB2 C. kunzei CBS 118556 DQ243791 – – – – – C. leucosperma CFCC 89622 KR045616 KR045698 KU710988 KU710944 KU710911 KR045657 C. longiostiolata MFLUCC 16-0628* KY417734 KY417768 KY417700 KY417802 – – C. longispora C. lumnitzericola CBS 144236* MFLUCC 17-0508* MG971905 MG975778 – MH253453 MG972054 MH253457 – MH253461 MG971615 – MG971764 – C. mali CFCC 50028 MH933641 MH933675 MH933548 MH933606 MH933513 MH933577 C. melnikii MFLUCC 15-0851* KY417735 KY417769 KY417701 KY417803 – – C. mougeotii ATCC 44994 AY347329 – – – – – C. multicollis CBS 105.89* DQ243803 – – – – – C. myrtagena CBS 116843* AY347363 – – – – – C. nitschkii CMW 10180* AY347356 – – – – – C. nivea MFLUCC 15-0860 KY417737 KY417771 KY417703 KY417805 – – C. oleicola CBS 144248* MG971944 – MG972098 – MG971660 MG971752 C. palm CXY 1280* JN411939 – – – KJ781297 – C. parakantschavelii MFLUCC 15-0857* KY417738 KY417772 KY417704 KY417806 – – C. parapersoonii T28.1* AF191181 – – – – – C. parapistaciae CBS 144506* MG971804 – MG971954 – MG971519 MG971669 C. paratranslucens MFLUCC 16-0506* KY417741 KY417775 KY417707 KY417809 – – C. pini C. pistaciae CBS 224.52* CBS 144238* AY347316 MG971802 – – – MG971952 – – – MG971517 – MG971667 C. platanicola MFLU 17-0327* MH253451 MH253452 MH253449 MH253450 – – C. platycladi CFCC 50504* MH933645 MH933679 MH933552 MH933610 MH933516 MH933581 C. platycladicola CFCC 50038* KT222840 MH933682 MH933555 MH933613 MH933519 MH933584 C. plurivora CBS 144239* MG971861 – MG972010 – MG971572 MG971726 C. populicola CBS 144240* MG971891 – MG972040 – MG971601 MG971757 C. populina CFCC 89644 KF765686 KF765702 KU711007 KU710969 KU710930 KR045681 C. predappioensis MFLUCC 17-2458* MG873484 MG873480 – – – – C. predappioensis MFLU 17-0327 MH253451 MH253452 MH253449 MH253450 – – C. prunicola MFLU 17-0995* MG742350 MG742351 MG742353 MG742352 – – C. pruinopsis CFCC 50034* KP281259 KP310806 KP310836 KU710970 KP310849 KP310819 C. pruinosa CBS 201.42 DQ243801 – – – – – C. punicae CBS 144244 MG971943 – MG972091 – MG971654 MG971798 C. quercicola MFLUCC 14-0867* MF190129 MF190073 – – – – C. rhizophorae MUCC302 EU301057 – – – – – C. ribis C. rosae CBS 187.36 MFLUCC 14-0845* DQ243810 MF190131 – MF190075 – – – – – – – – C. rostrata CFCC 89909* KR045643 KR045722 KU711009 KU710974 KU710932 KR045684 C. rusanovii MFLUCC 15-0854* KY417744 KY417778 KY417710 KY417812 – – C. salicacearum MFLUCC 16-0509* KY417746 KY417780 KY417712 KY417814 – – C. salicicola MFLUCC 14-1052* KU982636 KU982635 KU982637 – – – C. salicina MFLUCC 15-0862* KY417750 KY417784 KY417716 KY417818 – – C. salicina MFLUCC 15-0862* KY417750 KY417784 KY417716 KY417818 – – C. schulzeri CFCC 50040 KR045649 KR045728 KU711013 KU710980 KU710936 KR045690 C. sibiraeae CFCC 50045* KR045651 KR045730 KU711015 KU710982 KU710938 KR045692 C. sophorae CFCC 89598 KR045654 KR045733 KU711018 KU710985 KU710941 KR045695 C. sophoricola CFCC 89595* KR045655 KR045734 KU711019 KU710986 KU710942 KR045696 C. sophoriopsis CFCC 89600* KR045623 KP310804 KU710992 KU710951 KU710915 KP310817 123 Fungal Diversity Table 3 (continued) Species Isolate no GenBank accession numbers ITS LSU ACT RPB2 tef1 TUB2 C. sorbi MFLUCC 16-0631* KY417752 KY417786 KY417718 KY417820 – – C. sorbicola MFLUCC 16-0584* KY417755 KY417789 KY417721 KY417823 – – C. spiraeae CFCC 50049* MG707859 MG707643 MG708196 MG708199 – – C. tamaricicola C. tanaitica CFCC 50508* MFLUCC 14-1057* MH933652 KT459411 MH933687 KT459412 MH933560 KT459413 MH933617 – MH933523 – MH933588 – C. thailandica MFLUCC 17-0262* MG975776 MH253455 MH253459 MH253463 – – C. tibouchinae CPC 26333* KX228284 KX228335 – – – – C. translucens CXY 1351 KM034874 – – – – KM034895 C. ulmi MFLUCC 15-0863* KY417759 – – – – – C. valsoidea CMW 4309* AF192312 – – – – – C. variostromatica CMW 6766* AY347366 – – – – – C. vinacea CBS 141585* KX256256 – – – KX256277 KX256235 C. viticola CBS 141586* KX256239 – – – KX256260 KX256218 C. xylocarpi MFLUCC 17-0251* MG975775 MH253462 MH253462 MH253462 – – Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold compare with other species in Cyphellophora (Yang et al. 2018). There are 26 epithets of Cyphellophora in Index Fungorum (2019). Yang et al. (2018) clarified 23 species in this genus. To properly delineate these species, phylogenetic studies using multi-loci sequences (ITS, LSU, RPB1 and TUB2) and the secondary structures of ITS analyses are needed (Réblová et al. 2013; Feng et al. 2014; Gao et al. 2014; Yang et al. 2018). Molecular based identification and diversity Based on SSU and LSU sequence data, Cyphellophora clustered in a well-supported clade within the Chaetothyriales (Feng et al. 2014). Generic and species delimitation with morphological characters, ecological traits, host distribution and phylogenetic analyses using the internal transcribed spacer region (ITS), the partial btubulin gene (TUB2), the nuclear large subunit rDNA gene (LSU) and the DNA dependent RNA polymerase II largest subunit (RPB1) were recently performed (Feng et al. 2014; Gao et al. 2014). The present study reconstructs the phylogeny of Cyphellophora based on analyses of a combined ITS, TUB2, LSU and RPB1 sequence data (Table 4, Fig. 9). The phylogenetic tree in this study is updated with recently introduced Cyphellophora species and corresponds to previous studies (Feng et al. 2014; Gao et al. 2014). Cyphellophoroa indica and C. taiwanensis lack sequences in GenBank (4/7/2019). Cyphellophoroa hylomeconis was synonymized as Camptophora hylomeconis and C. eugeniae was synonymized as Aphanophora eugeniae (Réblová et al. 2013). Cyphellophoroa eucalypti were synonymized as C. guyanensis (Feng et al. 2014). Therefore, these species were not included in the present phylogenetic analyses (Fig. 9). Recommended genetic markers (genus level)—LSU and SSU Recommended genetic markers (species level)—ITS, LSU, TUB2, RPB1 and secondary (2D) structure of ITS analyses LSU is useful for preliminary identification at the generic level (Feng et al. 2014). Réblová et al. (2013) resolved Cyphellophora and Phialophora as close relatives within the Chaetothyriales, although both genera were paraphyletic based on analysis of ITS, TUB2 and nuc28S rDNA sequence data. It is recommended to use a combination of ITS, LSU, TUB2, RPB1 and secondary (2D) structure of ITS analyses (Réblová et al. 2013; Feng et al. 2014; Gao et al. 2014) in order to identify to the species level. Accepted number of species: 24 species References: Vries 1962, 1986; Matsushima 1987; Walz and de Hoog 1987; Decock et al. 2003; Crous et al. 2013, 2016; Réblová et al. 2013; Feng et al. 2014; Gao et al. 2014; Madrid et al. 2016; Yang et al. 2018 (morphology, phylogeny) Cyttaria Berk., Trans. Linn. Soc. London 19:40 (1842) This genus is geographically restricted to South America (Argentina and Chile) and Southeastern Australasia (including Tasmania, and New Zealand) (Peterson and Pfister 2010). Cyttaria species are found in the secondary phloem and xylem, cambium and cortex of the hosts. They produce 123 Fungal Diversity Fig. 8 Phylogenetic tree generated by maximum parsimony analysis of combined ITS, LSU, ACT and RPB2 sequence data of Cytospora species. Related sequences were obtained from GenBank. One hundred and eleven strains are included in the analyses, which comprised 2266 characters including gaps. The tree was rooted with Diaporthe vaccinii (CBS 160.32). The maximum parsimonious dataset consisted of 1358 constant, 596 parsimony-informative and 123 312 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 3836 steps (CI = 0.364, RI 0.649, RC = 0.236, HI = 0.636) in the first tree. MP and ML bootstrap values C 50% and Bayesian posterior probabilities C 0.90 are shown respectively near the nodes. The scale bar indicates 10 changes per site. Ex-type strains are in bold Fungal Diversity Fig. 8 continued trunk and branch cankers that arise due to localized, stimulated cambial activity attributed to the presence of hyphae of Cyttaria (Wilson 1907; Gutierrez de Sanguinetti 1988). Cyttaria species are considered as weak parasites (Gamundı́ and De Lederkremer 1989). Classification—Leotiomycetes, Leotiomycetidae, Cyttariales, Cyttariaceae Type species—Cyttaria darwinii Berk., Trans. Linn. Soc. London 19:40 (1842) Distribution—Argentina, Australia, Chile, New Zealand, Tasmania. Disease symptoms—Canker, galls These species are known to cause two types of cankers: globose and longitudinal. Globose cankers arise from 123 Fungal Diversity Table 4 Details of the Cyphellophora isolates used in the phylogenetic analyses Species Isolate/voucher no ITS LSU RPB1 TUB2 Cyphellophora ambigua CBS 235.93* JQ766431 JQ766480 JQ766386 JQ766340 C. artocarpi CGMCC3.17496* KP010367 KP122930 KP122920 KP122925 C. catalaunica CPC 22929* HG003670 HG003673 – – C. chlamydospora CBS 127581 (= FMR 10878) * HG003674 HG003675 – – C. europaea CBS 101466* JQ766443 KC455259 JQ766395 JQ766365 C. europaea CBS 218.78 JQ766441 JQ766488 JQ766393 JQ766366 C. europaea CBS 129.96 JQ766440 JQ766487 JQ766392 JQ766364 C. filicis KUMCC 18-0144 MK404056 MK404052 – – C. fusarioides CBS 130291* JQ766439 KC455252 JQ766391 JQ766363 C. gamsii CPC 25867* KX228255 KX228307 – KX228381 C. guyanensis C. guyanensis MUCL 43737* CBS 124764 KC455240 GQ303274 KC455253 GQ303305 – – KC455223 – C. guyanensis CBS 126014 JQ766434 JQ766483 JQ766389 JQ766339 C. jingdongensis IFRDCC 2659* MF285234 MF285236 – – C. laciniata CBS 190.61* JQ766423 JQ766472 JQ766378 JQ766329 C. laciniata CBS 174.79 JQ766422 JQ766471 JQ766377 JQ766328 C. laciniata CBS 239.91 JQ766424 JQ766473 JQ766379 JQ766330 C. livistonae CPC19433 KC005774 KC005796 – – C. musae CGMCC3.17497* KP010370 KP122932 KP122922 KP122927 C. musae GLGZXJ9B KP010368 KP122931 KP122923 KP122926 C. musae GLMMZZ4 KP010369 KP122934 KP122921 KP122928 C. olivacea CBS 123.74* KC455248 KC455261 – KC455231 C. olivacea CBS 122.74 KC455247 KC455260 – KC455230 C. oxyspora CBS 698.73* JQ766450 KC455262 JQ766402 KC455232 C. oxyspora CBS 416.89 JQ766449 JQ766497 JQ766401 JQ766374 C. pauciseptata CBS 284.85* JQ766466 JQ766515 JQ766415 JQ766360 C. phyllostachidis C. pluriseptata CGMCC3.17495* CBS 286.85* KP010371 JQ766429 KP122933 KC455255 KP122924 JQ766384 KP122929 JQ766335 C. pluriseptata CBS 109633 JQ766430 JQ766479 JQ766385 JQ766336 C. reptans CBS 113.85* JQ766445 JQ766493 JQ766397 JQ766370 C. reptans CBS 152.90 JQ766446 JQ766494 JQ766398 JQ766371 C. reptans CBS 458.92 JQ766447 JQ766495 JQ766399 JQ766372 C. reptans CBS120903 JQ766448 JQ766496 JQ766400 JQ766373 C. sessilis CBS 243.85* EU514700 EU514700 – KC455234 C. sessilis CBS 238.93 AY857541 KF928523 – KF928587 C. suttonii CBS 449.91* JQ766459 KC455256 – KC455226 C. suttonii FMR 10589 KU705828 KU705845 – – C. vermispora CBS 228.86* KC455244 KC455257 JQ766381 JQ766332 C. vermispora CBS 122852 JQ766427 JQ766476 JQ766382 JQ766333 C. vermispora CBS 227.86 JQ766425 JQ766474 JQ766380 JQ766331 Cladophialophora immunda CBS 834.96 EU137318 KC809990 – EU137203 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold 123 Fungal Diversity Fig. 9 Phylogram generated from RAxML analysis based on combined sequences of ITS, LSU, RPB1 and TUB2 sequences of all accepted species of Cyphellophora. Forty-one strains are included in the analyses, which comprise 2514 characters including gaps. The tree was rooted with Cladophialophora immunda (CBS 834.96). Tree topology of the ML analysis was similar to the MP and BYPP analyses. The best scoring RAxML tree with a final likelihood value of - 5928.387430 is presented. The matrix had 337 distinct alignment patterns, with 12.44% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.234866, C = 0.250597, G = 0.284325, T = 0.230211; substitution rates AC = 1.492532, AG = 2.025910, AT = 2.769660, CG = 1.674732, CT = 8.545312, GT = 1.000000; gamma distribution shape parameter a = 0.136482. RAxML and maximum parsimony bootstrap support value C 50% are shown respectively near the nodes. Bayesian posterior probabilities C 0.95 (BYPP) indicated as thickened black branches. Ex-type strains are in bold growth mainly in the transverse axis of the branch while longitudinal cankers arise from growth mainly along the long axis (Rawlings 1956; Gamundi 1971). Development of perennial galls on branches and stems may lead to malformation and occasional death of branches (Gadgil 1985). Hosts—Nothofagus spp. Morphological based identification and diversity Ascomata of Cyttaria species are orange, pitted apothecia similar to deeply dimpled golf balls. Each fruiting body is composed of 1–200 apothecia immersed in a sterile fleshygelatinous stroma. Asci are 8-spored, inoperculate and amyloid. Ascospores are uninucleate, subglobose to ovoid, smooth to rugulose, at first hyaline to yellowish but later becoming pigmented (Mengoni 1986; Peterson et al 2010). Molecular based identification and diversity The first phylogenetic analysis which included Cyttaria was done by Gargas and Taylor (1995) showing its relationship with other discomycetes. Wang et al. (2006) showed its placement within Leotiomycetes using combined analysis of SSU, LSU and 5.8S rDNA gene sequence data and then confirmed by Ekanayaka et al. (2017). Peterson and Pfister (2010) did large scale phylogeny for Cyttaria including all accepted 12 species in the genus using sequence data of partial nucSSU, nucLSU and mtSSU rRNA, as well as tef1. They found Cyttaria to be a strongly supported clade and suggested a close relationship between Cyttaria and some members of the Helotiales (Cordierites, Encoelia, Ionomidotis and Chlorociboria) (Peterson and Pfister 2010). The present study reconstructs the phylogeny of Cyttaria based on analyses of a combined 123 Fungal Diversity Table 5 Details of Cyttaria isolates used in the phylogenetic analyses Species Isolate/voucher no LSU SSU mtSSU C. berteroi Isolate 16 EU107205 EU107178 EU10723 C. darwinii Isolate 40 EU107207 EU107180 EU107236 C. darwinii Isolate 14 EU107208 EU107181 – C. darwinii Isolate 57 EU107206 EU107179 EU107235 C. darwinii Isolate 45 EU107209 – – C. darwinii Isolate 50 EU107211 – – C. darwinii Isolate 49 EU107210 – – C. espinosae Isolate 187 – EU107183 EU107238 C. espinosae Isolate 92 EU107212 EU107182 EU107237 C. exigua Isolate 77 EU107214 EU107185 EU107240 C. exigua Isolate 76 EU107213 EU107184 EU107239 C. gunnii Isolate 138 – EU107189 EU107242 C. gunnii Isolate 127 EU107215 EU107186 EU107241 C. gunnii Isolate 136 – EU107188 – C. gunnii C. hariotii Isolate 132 Isolate 44 – EU107217 EU107187 EU107194 – EU107245 C. hariotii Isolate 55 EU107218 EU107195 EU107246 C. hariotii Isolate 65 EU107223 – – C. hariotii Isolate 64 EU107222 – – C. hariotii Isolate 63 EU107221 – – C. hariotii Isolate 62 EU107220 – – C. hariotii Isolate 51 EU107219 – – C. hookeri Isolate 60 EU107227 – – C. hookeri Isolate 59 EU107226 – – C. hookeri Isolate 80 EU107228 – – C. hookeri Isolate 61 EU107225 EU107197 – C. hookeri Isolate 58 EU107224 EU107196 – C. johowii Isolate 73 EU107229 EU107198 – C. johowii Isolate 74 EU107230 EU107199 – C. nigra Isolate 100 EU107232 EU107201 EU107248 C. nigra C. septentrionalis Isolate 97 Isolate 199 EU107231 – EU107200 EU107203 EU107247 EU107249 C. septentrionalis Isolate 85 – EU107202 – LSU, SSU and mtSSU sequence data (Table 5, Fig. 10). The phylogenetic tree is updated with recently introduced Cyttaria species and corresponds to previous studies (Feng et al. 2014; Gao et al. 2014). Recommended genetic markers (genus level)—ITS, LSU Recommended genetic markers (species level)—nucSSU, nucLSU, mitSSU rRNA, and tef1 Combined nucSSU, nucLSU, mitSSU rRNA, and tef1 can resolve almost all species of Cyttaria currently known from sequence data (Peterson et al 2010). Accepted number of species: There are 21 epithets in Index Fungorum (2019). However, 12 species have molecular data and are treated as accepted. 123 References: Mengoni 1986, Peterson et al 2010 (morphology); Peterson and Pfister (2010), Ekanayaka et al. 2017 (morphology, phylogeny). Dactylonectria L. Lombard & Crous, in Lombard et al., Phytopath. Mediterr. 53(3): 523 (2014) The genus Dactylonectria was introduced by Lombard et al. (2014) for a group of species which were previously treated in Ilyonectria (Chaverri et al. 2011; Cabral et al. 2012a, b, c). In morphology, Dactylonectria resembles Ilyonectria and Neonectria but can be distinguished by their characteristic ovoid to obpyriform, smooth to finely warted, dark-red ascomata with a papillate ostiolar region at the apex (Lombard et al. 2014; Gordillo and Decock Fungal Diversity Fig. 10 Phylogram generated from RAxML analysis based on combined sequences of LSU, SSU and mtSSU sequences of all the accepted species of Cyttaria. Related sequences were obtained from GenBank. Thirty-four strains are included in the analyses, which comprise 3480 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 Chlorociboria cf. aeruginosa (OSC 100056). The best scoring RAxML tree with a final likelihood value of - 7505.900855 is presented. The matrix had 360 distinct alignment patterns, with 39.17% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.256, C = 0.214, G = 0.280, T = 0.250; substitution rates AC = 1.190197, AG = 1.207782, AT = 0.373130, CG = 0.681125, CT = 3.724394, GT = 1.000000; gamma distribution shape parameter a = 0.020000. RAxML and maximum parsimony bootstrap support value C 50% (BT) are shown respectively near the nodes 2018). Species of this genus are mostly associated with Vitis sp., while some species are also recorded from other hosts (Farr and Rossman 2019). Classification—Sordariomycetes, Hypocreomycetidae, Hypocreales, Nectriaceae Type species—Dactylonectria macrodidyma (Hallen, Schroers & Crous) L. Lombard & Crous, in Lombard et al., Phytopath. Mediterr. 53(3): 527 (2014) Distribution—Worldwide Disease symptoms—Black foot disease, black root rot Characteristic symptoms of black foot disease include a reduction in root biomass and root hairs with sunken and necrotic lesions (Halleen et al. 2006). Severe necrosis of the root system results in stunting, wilting, leaf chlorosis, browning and leaf drop prior to death (Parkinson et al. 2017). Dactylonectria alcacerensis, D. estremocensis, D. macrodidyma, D. novozelandica, D. pauciseptata, D. pinicola, D. torresensis and D. vitis are associated with black foot disease of grapevine (Cabral et al. 2012a; Lombard et al. 2014) (Fig. 11). Hosts—Abies sp., Annona cherimola, Anthrium sp., Arbutus unedo, Cistus albidus, Crataegus azalous, Erica melanthera, Eriobotrya japonica, Ficus sp., Fragaria sp., Hordeum vulgare, Ilex aquifolium, Juglans regia, Juniperus phoenicea, Lonicera sp., Myrtus communis, Persea americana, Picea glauca, Pinus sp., Pistacia lentiscus, 123 Fungal Diversity Fig. 11 Symptoms of black foot disease on Vitis spp. a, b dead plants and stunted growth of grapevine. c, e Infection of rootstock. d Blocked xylem vessels. f Black streak (Courtesy of Halleen) Prunus domestica, Pyracantha sp., Quercus sp., Rosmarinus officinalis, Santolina chamaecyparissus and Vitis sp. Morphological based identification and diversity Lombard et al. (2014) accepted ten species in Dactylonectria based on ITS, LSU, TUB2 and tef1 sequence data and morphological characters. Later, Gordillo and Decock (2018) introduced another four species to the genus based on morphology and sequence data. Fourteen Dactylonectria species have been described with DNA sequence data in GenBank. Dactylonectria species produce cylindrocarpon-like asexual morphs, several of which were previously treated in Ilyonectria (Lombard et al. 2014). Dactylonectria species were distinguished mainly by phylogenetic inference and using unique fixed single nucleotide polymorphisms (SNP’s) rather than morphological characters (Lombard et al. 2014; Gordillo and Decock 2018). Molecular based identification and diversity Lombard et al. (2014) re-evaluated genera with cylindrocarpon-like asexual morphs based on multi-gene phylogeny of ITS, LSU, TUB2 and tef1 genes. Gordillo and Decock (2018) analysed His3 together with latter gene regions, for delimiting the species in Dactylonectria. Lombard et al. (2015) also supported the fact that Dactylonectria is monophyletic and distinct from Ilyonectria. In this study, we reconstruct the phylogeny of Dactylonectria based on analyses of a combined ITS, LSU, TUB2 and tef1 sequence 123 data (Table 6, Fig. 12). The phylogenetic tree is updated with recently introduced Dactylonectria species and corresponds to previous studies (Lombard et al. 2014, 2015; Gordillo and Decock 2018). Recommended genetic markers (genus level)—ITS, LSU, TUB2, tef1 Recommended genetic markers (species level)—TUB, tef1 Accepted number of species: 14 species References: Cabral et al. 2012a, b; Halleen et al. 2004, Schroers et al. 2008; Lombard et al. 2014; Gordillo and Decock 2018 (morphology, phylogeny). Entoleuca Syd., Annls mycol. 20(3/4):186 (1922) The genus Entoleuca Syd. (Xylariaceae) consists of saprobic and plant pathogenic species distributed in Europe. Entoleuca mammata causes canker diseases (commonly known as Hypoxylon canker) on Malus sp. (Rosaceae), Populus sp., Salix sp. (Salicaceae) and Sorbus sp. (Rosaceae) (Shaw 1973; Callan 1998; Kasanen et al. 2004; Eriksson 2014) and also occurs as a saprobe on decaying tree trunks. The species are distributed in terrestrial habitats in temperate regions. The genus is characterized by its known sexual morph. It is characterized by partially embedded solitary or aggregated orbicular stroma, that has a whitish surface when young and dark surface at maturity, papillate ostiole; multiple, monostichous and embedded ascomata in stromata; 8-spored, unitunicate asci that are cylindrical, long pedicellate, with J? apical ring bluing in Melzer’s reagent and uniseriate, unicellular, Fungal Diversity Table 6 Details of the Dactylonectria isolates used in the phylogenetic analyses Species Isolate/voucher no ITS LSU TUB2 tef1 Campylocarpon fasciculare CBS 112613* AY677301 HM364313 AY677221 JF735691 Dactylonectria alcacerensis CBS 129087* JF735333 KM231629 AM419111 JF735819 D. anthuriicola CBS 564.95* JF735302 KM515897 JF735430 JF735768 D. amazonica MUCL55433* MF683707 MF683727 MF683644 MF683665 D. ecuadoriense MUCL55424* MF683704 MF683724 MF683641 MF683662 D. estremocencis CBS 129085* JF735320 KM231630 JF735448 JF735806 D. hordeicola CBS 162.89* AM41906 KM515898 AM419084 JF735799 D. macrodidyma CBS 112615* AY677290 KM515900 AY677233 JF735836 D. novozelandica CBS 112608* AY677288 KM515901 AY677235 JF735821 D. palmicola MUCL55426* MF683708 MF683728 MF683645 MF683666 D. pauciseptata CBS 120171* EF607089 KM515903 EF607066 JF735776 D. pinicola CBS 173.37* JF735319 KM515905 JF735447 JF735803 D. polyphaga MUCL55209* MF683689 MF683710 MF683626 MF683647 D. torresensis CBS 129086* JF735362 KM231631 JF735492 JF735870 D. vitis CBS 129082* JF735303 KM515907 JF735431 JF735769 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold Fig. 12 Phylogram generated from RAxML analysis based on combined sequences of ITS, LSU, TUB and tef1 sequences of all the accepted species of Dactylonectria. Related sequences were obtained from GenBank. Fifteen 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 Campylocarpon fasciculare (CBS 112613). Tree topology of the ML analysis was similar to the BI. 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. RAxML and maximum parsimony bootstrap support value C 50% are shown respectively near the nodes. Bayesian posterior probabilities C 0.95 (BYPP) indicated as thickened black branches. Ex-type strains are in bold ellipsoidal inequilateral, brown, with straight to oblique germ slit ascospores (Rogers and Ju 1996; Daranagama et al. 2018). Daranagama et al. (2018) provided an identification key with emphasis on the coarsely papillate ostiole in Entoleuca. Sydow and Petrak (1922) introduced the genus with E. callimorpha as the type species. Until 1994, Hypoxylon mammatum was considered a similar taxon to E. callimorpha. However, Læssøe and Spooner (1994) and Læssøe (1994) treated H. mammatum as a separate, synonym to Rosellinia. Based on these taxonomic confusions, Rogers and Ju (1996) revised the type, authentic and other specimens and re-established the genus Entoleuca. Classification—Sordariomycetes, Xylariomycetidae, Xylariales, Xylariaceae Type species—Entoleuca callimorpha Syd., in Sydow & Petrak, Annls mycol. 20(3/4):186 (1922) Distribution—Austria, Canada, Poland, Sweden, USA Disease symptoms—Canker 123 Fungal Diversity Symptoms may vary on the stage of disease development. Young cankers appear as slightly sunken, yellowish orange areas with irregular margins. Later, the outer-most bark within the canker breaks out in blisters exposing a powdery grey mat of fungal tissue and conidia. Then the patches of bark start to flake off making the canker rough and black in the centre. Advancing margins of the enlarging cankers become yellowish orange (Ostry 2013). Hosts—Known from Malus sylvestris, Populus sp., Salix sp. and Sorbus aucuparia. Recommended genetic markers (genus level)—LSU and ITS Recommended genetic markers (species level)—RPB2 and TUB2 Combined LSU, ITS, RPB2 and TUB2 provide a satisfactory resolution for resolving species. Accepted number of species: Three species References: Sydow and Petrak 1922; Rogers and Ju 1996; Ju et al. 2004 (morphology), Daranagama et al. 2018 (morphology, phylogeny). Morphological based identification and diversity Eutiarosporella Crous, in Crous et al., Phytotaxa 202(2): 85 (2015) Eutiarosporella was introduced by Crous et al. (2015) and is typified by Eutiarosporella tritici (B. Sutton & Marasas) Crous on Triticum aestivum from South Africa. The genus was named on account of its similarity to Tiarosporella Höhn. (Crous et al. 2006). Eutiarosporella species are coelomycetes that are saprobes or pathogens which occur in terrestrial habitats (Crous et al. 2015; Thynne et al. 2015; Li et al. 2016). Eutiarosporella species have been reported from Celtis africana (Rosales), Triticum aestivum (Poales), Acacia karroo (Fabales) and Dactylis glomerata (Poales) (Thambugala et al. 2014; Crous et al. 2015). On wheat, it causes the economically important disease known as white grain disorder (Thynne et al. 2015). Several studies have reported this genus on woody hosts as a saprobe (Jami et al. 2012, 2014; Dissanayake et al. 2016). Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Eutiarosporella tritici (B. Sutton & Marasas) Crous, in Crous et al., Phytotaxa 202(2):85 (2015) Distribution—Worldwide Disease symptoms—White grain disorder of wheats White grain disorder shrivels and discolours (white to light grey) wheat grain (Thynne et al. 2015). Affected grains are more brittle and can break during harvesting. Infected spikelets of green heads may show bleaching appreance or grey discolouration. At first, the bleached florets may show blue-gray ‘highlights’. Rachis of affected heads and the upper peduncle may show a brownish discolouration (Thynne et al. 2015). Even though species of this genus have been found to be associated with several hosts other than wheat, their diseases have not been described. Hosts—Acacia karroo, Arrhenatherum elatius, Avenella flexuosa, Celtis africana, Dactylis glomerata, Triticum aestivum and Vachelloa karroo (Farr and Rossman 2019). Currently, the genus comprises three species: E. callimorpha, E. ellisii and E. mammata (Sydow and Petrak 1922; Rogers and Ju 1996; Ju et al. 2004; Index Fungorum 2019). Due to the presence of clear papillate ostioles, they have been distinguished from closely related genera such as Amphirosellinia, Nemania, and Rosellinia. Molecular data are only available for E. mammata, which is the most important species in the genus as a pathogen. Rogers and Ju (1996) observed that there are no distinguishing morphological differences among E. mammata isolates from different hosts. However, there is a high polymorphism, but no major phylogenetic differences among the isolates from Europe (Kasanen et al. 2004). Ju et al. (2004) introduced E. ellisii based on characterizations of ascospore and germ slit. Therefore, a combination of morphological and phylogenetic analyses are needed for species delimitation of Entoleuca. Molecular based identification and diversity Several recent studies have focused on the molecular phylogeny of Entoleuca, especially E. mammata. Phylogenetic based population studies revealed that higher polymorphism occurs in North American than in Europe (Kasanen et al. 2004). The sterile mycelia associated with Pinus tabulaeformis and its ITS-based phylogenetic analyses revealed that the genus Entoleuca clusters in Xylariaceae and is closely related to Nemania (Guo et al. 2003). Daranagama et al. (2018) revisited the family Xylariaceae and due to the morphological differences and conidial state characters, they suggested that it is useful to maintain the taxa as distinct genera. Daranagama et al. (2018) and Wendt et al. (2018) conducted multi-gene phylogenetic analyses using ITS, LSU, RPB2 and TUB2 and revealed that E. mammata clusters with Rosellinia corticium with high support. Due to the lack of molecular data from other species and other gene regions, it is difficult to place Entoleuca in an appropriate family. In this study, we included the available sequences of Entoleuca in the analysis done for Rosellinia (Table 7, Fig 13). 123 Morphological based identification and diversity Eutiarosporella is characterized by hairy conidiomata with long necks, and holoblastic conidiogenesis, features which Fungal Diversity Table 7 Details of the Entoleuca and Rosellinia isolates used in the phylogenetic analyses Species Isolate/voucher no ITS LSU RPB2 Coniolariella gamsii CBS 114379* GU553325 GU553329 N/A C. hispanica ATCC MYA4453* GU553323 GU553353 N/A C. limonispora CBS 382.86 KF719199 KF719211 N/A C. limonispora var. australis AV1L2-3 KP101193 N/A N/A C. limonispora var. australis AH24323 AY908997 N/A N/A Entoleuca mammata JDR 100 GU300072 N/A GQ844782 E. mammata ATCC 58108 AF201713 N/A N/A E. mammata Osterby 1 AF176983 N/A N/A Rosellinia abscondita CBS 447.89 FJ175180 KF719208 N/A R. aquila MUCL 51703 KY610392 KY610460 KY624285 R. arcuate CBS347.29 AB017660 N/A N/A R. asperata var. minor CBS 138641* KY941107 N/A N/A R. australiensis CBS 142160* KY979742 KY979797 N/A R. britannica CBS 446.89 FJ175182 KF719209 N/A R. bunodes R. buxi CBS 347.36 JDR 99 AB609598 GU300070 KF719205 N/A N/A GQ844780 R. buxi ATCC 32869 AY909000 EF489467 N/A R. capetribulensis HKU(M) 17499* AY862570 N/A N/A R. acutispora CBS 138730 KY941108 N/A N/A R. chiangmaiensis MFLU 15-3524* KU246226 KU246227 N/A R. compacta NIAES:20565* AB430457 N/A N/A R. convexa GZUCC 13005* KF614036 N/A KP876561 R. convexa ZG-1-2-1 KR822145 N/A N/A R. corticium MUCL 51693 KC477236 KY610461 KY624229 R. desmazieri olrim153 AY805591 N/A N/A R. lamprostoma HAST 89112602 EF026118 N/A GQ844778 R. mammiformis CBS 445.89 KF719200 KF719212 N/A R. mearnsii MFLU 16-1382* KY514059 KY514060 KY514061 R. merrillii HAST 89112601* GU300071 N/A GQ844781 R. necatrix HAST 89062904 EF026117 AY083824 GQ844779 R. necatrix R. nectrioides CBS 349.36 CBS 449.89 AY909001 FJ175181 KF719204 KF719213 N/A N/A R. quercina ATCC 36702 AB017661 N/A N/A R. sanctaecruciana HAST 90072903 GU292824 N/A GQ844777 R. subiculata ATCC 58850 AY909002 EF489468 N/A R. thelena CBS 400.61 KF719202 KF719215 N/A R. truncatispora CBS 138732* KY941109 N/A N/A Xylaria bambusicola WSP 205* EF026123 AB376825 GQ844802 X. grammica HAST 479 GU300097 N/A GQ844813 X. hypoxylon CBS 122620* AM993141 KM186301 KM186302 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold are clearly distinguishable from Tiarosporella (Höhnel 1919; Crous et al. 2015). This genus is morphologically similar to Marasasiomyces (long-necked, hairy conidiomata, and holoblastic conidiogenesis), except that it forms conidiomata in clusters, which are not found in Marasasiomyces (Crous et al. 2015). Li et al. (2016) reported the sexual morph of Eutiarosporella in E. dactylidis for the first time from Avenella flexuosa (Poales). The sexual morph is characterised by globose ascomata, with a central ostiole, a two-layered peridium, hyphae-like pseudoparaphyses and hyaline, aseptate, fusoid to ovoid ascospores, with a mucilaginous sheath (Thambugala et al. 2014). 123 Fungal Diversity Fig. 13 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, LSU and RPB2 sequence data of Entoleuca and Rosellinia species. Related sequences were obtained from GenBank. Forty strains are included in the analyses, which comprise 2336 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 Xylaria bambusicola (WSP 205), X. grammica (HAST 479) and X. hypoxylon (CBS 122620). Tree topology of the ML analysis was similar to the MP. The best scoring RAxML tree with a final likelihood value of - 12521.202450 is presented. The matrix had 793 distinct alignment patterns, with 51.67% of undetermined characters or gaps. Estimated base 123 frequencies were as follows; A = 0.241655, C = 0.263843, G = 0.260086, T = 0.234416; substitution rates AC = 1.764265, AG = 4.237635, AT = 0.953946, CG = 1.541272, CT = 8.643978, GT = 1.000000; gamma distribution shape parameter a = 1.105097. The maximum parsimonious dataset consisted of constant 1567, 629 parsimony-informative and 140 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of two equally most parsimonious trees with a length of 2112 steps (CI = 0.545, RI = 0.668, RC = 0.364, HI = 0.455) in the first tree. RAxML and maximum parsimony bootstrap support value C 50% are shown respectively near the nodes. Ex-type strains are in bold Fungal Diversity Based on ITS and LSU sequence data, three species were initially included in this genus, E. africana (Jami et al.) Crous, E. tritici (B. Sutton & Marasas) Crous and E. urbis-rosarum (Jami et al.) Crous by Crous et al. (2015). Subsequently, E. darliae E. Thynne et al., E. tritici-australis E. Thynne, et al. and E. dactylidis (Thambug., Camporesi & K.D. Hyde) Dissan., Camporesi & K.D. Hyde were accommodated in the genus (Crous et al. 2015; Thynne et al. 2015; Li et al. 2016), which now comprises seven species (Dissanayake et al. 2016; Wijayawardene et al. 2017). Colony and conidial morphology are the primary characters to identify species within this genus. Colonies on nutrient-rich media (PDA or V8-OMA) grow rapidly (Thynne et al. 2015). However, we consider morphological characters alone are inadequate to identify species due to plasticity and overlapping of conidial dimensions. Therefore, incorporation of molecular data together with morphology is recommended. disease symptoms of their original plant hosts (Chaverri et al. 2011; Cabral et al. 2012a,c; Lombard et al. 2013, 2014; Aiello et al. 2014). Ilyonectria is a well-known genus causing black foot rot of grapevines in various countries (Halleen et al. 2003, 2004, 2006; Chaverri et al. 2011; Cabral et al. 2012a, b, c; Lombard et al. 2014). Classification—Sordariomycetes, Hypocreomycetidae, Hypocreales, Nectriaceae Type species—Ilonectria radicicola (Gerlach & L. Nilsson) P. Chaverri & Salgado, in Chaverri et al., Stud. Mycol. 68:71 (2011) Distribution—Worldwide Disease symptoms—Black foot disease, black root rot Symptoms are given under the genus Dactylonectria Hosts—Wide host range including plant genera in Amaryllidaceae, Aracaceae, Araliaceae, Cupressaceae, Fagaceae, Liliaceae, Myrtaceae, Pinaceae, Proteaceae, Rosaceae, Strelitziaceae and Vitaceae (Farr and Rossman 2019). Molecular based identification and diversity Morphological based identification and diversity Taxonomy of Eutiarosporella is largely based on DNA sequence data to reveal the phylogenetic relationships between the species (Crous et al. 2015; Thynne et al. 2015; Dissanayake et al. 2016; Li et al. 2016). According to studies by Crous et al. (2015), Thynne et al. (2015) and Li et al. (2016), ITS and LSU are the most suitable loci for delineation of species within the genus. The phylogram generated with sequences available in GenBank including ex-epitype sequences is provided in Fig. 14 (Table 8). Our phylogenetic analyses are in accordance with previous studies by Crous et al. (2015), Thynne et al. (2015), Dissanayake et al. (2016) and Li et al. (2016). The genus Ilyonectria was introduced based on I. radicicola as the type species, to accommodate Neonectria species belonging to the ‘‘N. radicicola’’ group (Booth 1959). This genus has asexual morphs and belonged to Booth’s Group 3 (chlamydospores and microconidia present, Booth 1966; Chaverri et al. 2011; Lombard et al. 2014). Molecular phylogenetic studies revealed that Ilyonectria, as originally conceived, was paraphyletic (Cabral et al. 2012a, c; Lombard et al. 2013, 2014). Conidial size, culture characters and molecular data enabled the separation of Ilyonectria species (Cabral et al. 2012a, c; Lombard et al. 2013, 2014). Recommended genetic markers (genus level)—LSU and SSU Recommended genetic markers (species level)—ITS and LSU Accepted number of species: Seven species. References: Crous et al. (2015), Thynne et al. (2015), Dissanayake et al. (2016), Li et al. 2016 (morphology, phylogeny). Molecular based identification and diversity Ilyonectria P. Chaverri & Salgado, in Chaverri et al., Stud. Mycol. 68:69 (2011) Species of Ilyonectria (Nectriaceae, Hypocreales) are important soil-borne pathogens of various woody and herbaceous plant hosts. Ilyonectria species are cosmopolitan and are found on a wide range of hosts (Chaverri et al. 2011). They are mostly associated with root diseases and stem cankers (Seifert et al. 2003; Halleen et al. 2004, 2006; Chaverri et al. 2011; Cabral et al. 2012a, b, c; Vitale et al. 2012; Lombard et al. 2013; Aiello et al. 2014). There are 23 species of Ilyonectria, all associated with Delineating between species of Ilyonectria can be achieved with histone (His3) gene region. The topologies of the phylogenetic tree (Fig. 15, Table 9) is similar to previous studies done on this genus (Cabral et al. 2012a; Lombard et al. 2014). Recommended genetic markers (genus level)—ITS, LSU, tef1, TUB2 Recommended genetic markers (species level)—tef1, TUB2, His3 Accepted number of species: 23 species References: Booth 1959, 1966 (morphology), Cabral et al. 2012a, b, c; Lombard et al. 2013, 2014 (morphology, phylogeny). Macrophomina Petr., Annls mycol. 21: 314 (1923) Species of Macrophomina are mostly pathogens that cause damping-off, seedling blight, collar rot, stem rot, charcoal rot, basal stem rot and root rot in many plant 123 Fungal Diversity species (Arora et al. 2001; Pal et al. 2001; Gupta et al. 2002; Sarr et al. 2014; Wijayawardene et al. 2017). The type species, Macrophomina phaseolina (Tassi) Goid., is a seed-borne polyphagous pathogen that affects more than 500 crop and non-crop species, including economically important crops, such as soybean, sunflower, common bean, peanut, corn, sorghum, cowpea and cotton (Gupta et al. 2002; Ndiaye et al. 2010; Sarr et al. 2014). Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Macrophomina phaseolina (Tassi) Goid., Annali Sper. agr., N.S. 1(3): 457 (1947) Distribution—Worldwide Disease symptoms—Charcoal rot, collar rot, damping off, root rot, seedling blight, stem rot, wilt Seedling damage can occur when infected seeds are planted. Infected plants may produce slightly smaller Fig. 14 Phylogram generated from maximum likelihood analysis based on combined LSU and ITS sequence data retrieved from GenBank. The tree is rooted in Tiarosporella paludosa (CPC 22701 and CBS 114650). Tree topology of the ML analysis was similar to the Bayesian analysis. The best scoring RAxML tree with a final likelihood value of - 7055.996836 is presented. The matrix had 380 distinct alignment patterns, with 40.12% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.229604, C = 0.264209, G = 0.282595, T = 0.223593; substitution rates AC = 1.357965, AG = 1.612491, AT = 0.913118, CG = 2.194420, CT = 5.121479, GT = 1.000000; gamma distribution shape parameter a = 0.137391. Maximum likelihood bootstrap support values greater than 60% are indicated above the nodes. Extype (ex-epitype) and voucher strains are in bold 123 leaflets than healthy plants and have reduced vigour. As the disease advances, leaflets turn yellow, wilt and turn brown (Adorada et al. 2018). A grey/silver discolouration can be observed in the roots and lower stem when the plants split open (Romero Luna et al. 2017; Koehler and Shew 2018; Meena et al. 2018). In charcoal rot, the abundant production of minute black sclerotia by the fungus causes the rotted tissues to become blackened. Infections on soybean lead to early maturation and incomplete pod filling (ElAraby et al. 2003; Yang and Navi 2005; Sarr et al. 2014). In peanut, it causes seed and seedling rots, wilt, root and stem rots, leaf spot and rotting of developing pods and seeds (Gupta et al. 2002; Deshwal et al. 2003). Hosts—This soil-borne fungus can infect more than 500 agricultural crops and weed species including, Fragaria, Glycine, Helianthus, Sorghum and Zea. Fungal Diversity Table 8 Details of the Eutiarosporella isolates used in the phylogenetic analyses Species Isolate/voucher no LSU ITS Botryobambusa fusicoccum MFLUCC 11-0657 JX646810 JX646793 B. fusicoccum MFLUCC 11-0143* JX646809 NR111793 Eutiarosporella africana CMW 38423* KC769990 KC769956 E. dactylidis MFLUCC 15-0915 KU246380 NR148093 Eutiarosporella dactylidis MFLUCC 13-0874 KM978948 KM978945 E. dactylidis MFLUCC 13-0276* KM978949 KM978944 E. urbis CMW 36477* JQ239420 NR111705 E. urbis-rosarum CMW 36479 JQ239422 JQ239409 E. urbis-rosarum CMW 36478 JQ239421 JQ239408 Marasasiomyces karoo CBS 1187.18* DQ377939 KF531828 Mucoharknessia anthoxanthi MFLUCC 15-0904* KU246379 NR148092 M. cortaderiae CPC 22208 KM108402 KM108375 M. cortaderiae CPC 19974* KM108401 NR148075 Sakireeta madreeya CBS 532.76* DQ377940 KC769960 Tiarosporella africana T. africana CMW 38425 CMW 38424 KC769992 KC769991 KC769958 KC769957 T. paludosa CPC 22701 KM108404 NR132907 T. paludosa CBS 114650* KM108403 KM108377 T. tritici CBS 118719* DQ377941 KC769961 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold Fig. 15 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, TEF, TUB, and His3 sequence data of Ilyonectria species. Twenty-three strains are included in the analyses, which comprise 2242 characters including gaps. The tree is rooted in Campylocarpon fasciculare. Tree topology of the ML analysis was similar to the one generated from BI (Figure not shown). The best scoring RAxML tree with a final likelihood value of - 9669.617830 is presented. The matrix had 507 distinct alignment patterns, with 5.11% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.219321, C = 0.325516, G = 0.222910, T = 0.230587; substitution rates AC = 0.215721, AG = 0.328038, AT = 0.225653, CG = 0.615208, CT = 5.798530, GT = 1.000000; gamma distribution shape parameter a = 0.518017. Maximum likelihood bootstrap support values C 60% and bayesian posterior probabilities C 95 (BYPP) are indicated above or near the nodes. Ex-type strains are in bold Morphological based identification and diversity species Macrophomina phaseolina and M. pseudophaseolina (Sarr et al. 2014). Morphological characteristics of M. Eight species names are recorded in Index Fungorum (2019), however, sequences are available for only two 123 Fungal Diversity phaseolina are mostly similar to M. pseudophaseolina, except that conidia of the latter are shorter. Colony and conidial morphology are the primary characters used to identify species within this genus (Ellis 1971, 1976; Simmons 1992). However, the connectivity of sexual and asexual morphs is not proven, as no sexual morph has been obtained from nature or culture (Crous et al. 2006; Wijayawardene et al. 2017, 2018). According to the morphological identifications, Macrophomina phaseolina has conidia with apical mucoid appendages as found in Tiarosporella (Sutton and Marasas 1976). Nevertheless, it can be distinguished from Tiarosporella in having conidia with apical mucoid appendages, per currently proliferating conidiogenous cells and dark brown (at maturity) conidia (Crous et al. 2006; Phillips et al. 2013). Morphologically M. phaseolina is similar to M. pseudophaseolina, except that conidia of the latter are shorter. sample of Macrophomina isolates from many hosts. According to the multi-gene analysis of SSU, LSU, ITS, tef1 and TUB2 genes in this study (Fig. 16, Table 10), the two species cluster in a well-supported clade with high bootstrap values (100% ML, 1.00 BYPP). The overall topology of our phylogeny tree is similar to previous studies. Recommended genetic markers (genus level)cosmopolitan genus, and—LSU and SSU Recommended genetic markers (species level)—ITS, tef1, ACT, CAL and TUB2 Accepted number of species: There are eight epithets in Index Fungorum (2019) However, two species have molecular data. Molecular based identification and diversity References: Crous et al. 2006; Phillips et al. 2013; Sarr et al. 2014, Wijayawardene et al. 2017 (morphology, phylogeny). Phillips et al. (2013) suggested that phylogenetic analysis of a combined SSU, LSU, ITS, tef1 and TUB2 genes provide better resolution. Sarr et al. (2014) used ITS, tef1, ACT, CAL and TUB2 sequence data representing a large Medeolaria Thaxt., Proc. Amer. Acad. Arts & Sci. 57(17): 432 (1922) The genus Medeolaria belongs to the family Medeolariaceae (Medeolariales, Leotiomycetes, Ascomycota). Table 9 Details of the Ilyonectria isolates used in the phylogenetic analyses Species Isolate/voucher no ITS Campylocarpon fasciculare CBS 112613 AY677301 Ilyonectria capensis CBS 132815* JX231151 I. coprosmae CBS 119606* JF735260 I. crassa CBS 139.30* I. cyclaminicola CBS 302.93* I. destructans tef1 tub2 His3 JF735691 AY677221 JF735502 JX231119 JX231103 JX231135 JF735694 JF735373 JF735505 JF735275 JF735723 JF735393 JF735534 JF735304 JF735770 JF735432 JF735581 CBS 264.65* AY677273 JF735695 AY677256 JF735506 I. europaea CBS 129078* JF735294 JF735756 JF735421 JF735567 I. gamsii I. leucospermi CBS 940.97 CBS 132809* AM419065 JX231161 JF735766 JX231129 AM419089 JX231113 JF735577 JX231145 I. liliigena CBS 189.49* JF735297 JF735762 JF735425 JF735573 I. liriodendri CBS 110.81* DQ178163 JF735696 DQ178170 JF735507 I. lusitanica CBS 129080 JF735296 JF735759 JF735423 JF735570 I. macroconidialis CBS 112615 AY677290 JF735836 AY677233 JF735647 I. mors-panacis CBS 306.35* JF735288 JF735746 JF735414 JF735557 I. palmarum CBS 135754* HF937431 HF922614 HF922608 HF922620 I. panacis CBS 129079* AY295316 JF735761 JF735424 JF735572 I. protearum CBS 132811* JX231157 JX231125 JX231109 JX231141 I. pseudodestructans CBS 129081 AJ875330 JF735752 AM419091 JF735563 I. robusta CBS 308.35* JF735264 JF735707 JF735377 JF735518 I. rufa CBS 156.47 AY677272 JF735730 AY677252 JF735541 I. strelitziae CBS 142253 * KY304649 KY304727 KY304755 KY304621 I. venezuelensis CBS 102032 * AM419059 JF735760 AY677255 JF735571 I. vredenhoekensis CBS 132807* JX231155 JX231123 JX231107 JX231139 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold 123 Fungal Diversity Medeolaria was introduced by Thaxter (1922) and typified with Medeolaria farlowii. Medeolaria species are pathogens of Medeola virginiana (Liliaceae). Currently, the known distribution of this genus is only from America. Classification—Leotiomycetes, Medeolariales, Medeolariaceae Type species—Medeolaria farlowii Thaxt., Proc. Amer. Acad. Arts & Sci. 57(17): 432 (1922) Distribution—America Disease symptoms—This fungus causes gall-like deformations on thickened, hypertrophic 9 parts below leaf whorls of herbaceous stems of the host tissue, in autumn. However, they are present not only in stem lesions of the host plant but in uninfected leaves, stems and rhizomes (Pfister et al 2013). Pfister et al. (2013) also showed the long-term perpetuation of the fungus in populations of the plant. They suggested the fungus remains as a systemic infection of vegetative plant parts and when the plant reproduces clonally, this infection is carried in populations of the host plant (Pfister et al 2013). Hosts—Magnolia spp. Morphological based identification and diversity This genus contains only a single species, Medeolaria farlowii Thaxter (1922), described from material collected from Magnolia. It produces erumpent, indefinite apothecia with a palisade layer of asci and paraphyses. An excipulum is absent or is a very thin layer. The hymenium layer forms fusiform swellings below and/or between the shortened internodes of the host plant. Ascospores are large, fusiform to naviculate, with a dark, striate outer wall. The asexual morph of this fungus is unknown (Korf 1973; Pfister and LoBuglio 2009; Ekanayaka et al 2017). Molecular based identification and diversity The first stable taxonomic placement for this genus was provided by Korf (1973) under the family Medeolariaceae, order Medeolariales within Leotiomycetes, according to its morphology. Recent phylogenetic studies (LoBuglio and Pfister 2010; Pfister et al 2013; Ekanayaka et al. 2017) confirmed its phylogenetic relationship with Leotiomycetes (Fig. 10), but the phylogenetic position within the class is unresolved. Recommended genetic marker (genus level)—ITS Recommended genetic marker (species level)—ITS ITS is the best single genetic marker for the genus Medeolaria (Pfister et al 2013). Pfister et al. (2013) provided primers, designed to specifically amplify ITS rDNA regions of Medeolaria farlowii. Accepted number of species: One species References: Korf 1973; LoBuglio and Pfister 2010; Pfister et al. 2013(morphology, phylogeny). Neonectria Wollenw., Annls mycol. 15(1/2):52 (1917) Neonectria is a cosmopolitan genus, and their asexual morphs are common in tropical and temperate regions (Chaverri et al. 2011). Neonectria species can be found on the bark of recently dead woody plants and sometimes on decaying herbaceous material (Samuels and Brayford 1990; Samuels and Brayford 1990, 1993, 1994; Rossman et al. 1999; Castlebury et al. 2006; Chaverri et al. 2011). Some species of Neonectria are plant pathogens causing cankers and other diseases on hardwood and coniferous trees (Castlebury et al. 2006; Rossman and Palm-Hernández 2008; Crane et al. 2009; Chaverri et al. 2011; Schmitz et al. 2017; Wenneker et al. 2017). Neonectria neomacrospora has been added to the European and Mediterranean Plant Protection Organization (EPPO) alert list (EPPO, 2019). Classification—Sordariomycetes, Hypocreomycetidae, Hypocreales, Nectriaceae Type species—Neonectria ramulariae Wollenw., Annls mycol. 15(1/2):52 (1917) Distribution—Worldwide Disease symptoms—Canker Dead shoots can be observed in the lower branches or all over the affected tree. Affected branches or trunks show canker and some may have abundant resin flow. When the canker girdles the affected area, part of the tree above the canker dies. Under humid conditions characteristic small, red fruiting bodies will be formed. Badly affected trees will eventually die (Castlebury et al. 2006). Beech (Fagus) bark disease is caused by N. coccinea, N. ditissima, N. fuckeliana and N. faginata. Cankers of fruit trees are caused by N. rugulosa and N. ditissima. Shoot dieback of Abies species are caused by N. neomacrospora (Castlebury et al. 2006; Rossman et al. 2008; Crane et al. 2009; Chaverri et al. 2011; Schmitz et al. 2017; Wenneker et al. 2017). Hosts—Wide host range including plant genera in Amaryllidaceae, Aracaceae, Araliaceae, Betulaceae, Ericaceae, Fagaceae, Lauraceae, Myrtaceae, Pinaceae, Proteaceae, Rosaceae, Sapindaceae and Vitaceae (Farr and Rossman 2019). Morphological based identification and diversity The genus Neonectria was established by Wollenweber (1917). The generic concept of Neonectria has been revised by different authors (Booth 1959; Samuels and Brayford 1994; Rossman et al. 1999). Rossman et al. (1999) accepted only three species (N. coccinia, N. galligena and N. ramulariae) in Neonectria. Subsequently, species were added to the genus based on morphology and/or phylogeny (Hirooka et al. 2005; Castlebury et al. 2006; Luo and Zhuang 2010a, b; Zhao et al. 2011; Lombard et al. 2014, 2015). However, some unrelated species were transferred to other genera based on molecular analyses 123 Fungal Diversity 123 Fungal Diversity b Fig. 16 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, LSU, SSU, tef1 and TUB2 sequences. Related sequences were obtained from GenBank. Forty-four strains are included in the analyses, which comprise 3477 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 Dothiorella iberica (CBS 113188 and CBS 115041). Tree topology of the ML analysis was similar to the MP and BI. The best scoring RAxML tree with a final likelihood value of - 12764.659013 is presented. The matrix had 898 distinct alignment patterns, with 28.31% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.238049, C = 0.253522, G = 0.272022, T = 0.236408; substitution rates AC = 1.121500, AG = 2.393284, AT = 1.053637, CG = 1.711098, CT = 4.682724, GT = 1.000000; gamma distribution shape parameter a = 0.545763. The maximum parsimonious dataset consisted of constant 2820, 575 parsimony-informative and 82 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of two equally most parsimonious trees with a length of 1490 steps (CI = 0.626, RI = 0.861, RC = 0.539, HI = 0.374) in the first tree. RAxML, maximum parsimony bootstrap support values C 65% and Bayesian posterior probabilities C 0.95 (BYPP) are shown respectively near the nodes. Ex-type strains are in bold and morphological data (Lombard et al. 2014, 2015). There are 31 species recognised in the genus, while 23 species have sequence data in GenBank (4/7/2019). Morphological characters (perithecial morphology, ascospore size, macroconidial morphology, presence or absence of microconidia and chlamydospores) along with DNA sequence analysis are appropriate for identification of Neonectria species (Brayford et al. 2004). Molecular based identification and diversity Since 2001, DNA sequence analysis has been used to clarify the taxonomy of Neonectria (Mantiri et al. 2001; Brayford et al. 2004; Halleen et al. 2004; Hirooka et al. 2005; Chaverri et al. 2011). Mantiri et al. (2001) and Brayford et al. (2004) used mtSSU rDNA sequence data to infer intrageneric relationships of some Neonectria and Cylindrocarpon species. Later, Halleen et al. (2004) used mtLSU rDNA, TUB2 and nrDNA ITS regions to separate some Cylindrocarpon species included in the N. mammoidea group. Chaverri et al. (2011) approached a comprehensive treatment of Cylindrocarpon and Neonectria based on combined loci analyses and morphological data. Chaverri et al. (2011) defined Neonectria sensu stricto within Nectriaceae with Cylindrocarpon sensu stricto based on multi-gene phylogeny of ITS, LSU, tef1, TUB2, ACT, and RPB1. The ITS, tef1 and TUB2 loci possess highly variable regions (Chaverri et al. 2011) and are important in species delimitation of Neonectria. Rossman et al. (2013) proposed to protect generic name Neonectria over Cylindrocarpon. Maharachchikumbura et al. (2015) considered Cylindrodendrum not to be congeneric with Neonectria and accepted Neonectria over Cylindrocarpon. This study reconstructs the phylogeny of Neonectria based on analyses of a combined ITS, LSU, tef1 and TUB2 sequence data (Table 11, Fig. 17). The phylogenetic tree is updated with recently introduced Neonectria species and corresponds to previous studies (Chaverri et al. 2011; Lombard et al. 2014; Mantiri et al. 2001). Recommended genetic markers (genus level)—LSU, ITS, tef1 and TUB2 Recommended genetic markers (species level)—ITS, tef1 and TUB2 Accepted number of species: 28 species References: Rossman et al. 1999 (morphology), Brayford et al. 2004; Hirooka and Kobayashi 2007; Chaverri et al. 2011; Lombard et al. 2014 (morphology, phylogeny). Neopestalotiopsis Maharachch., K.D. Hyde & Crous (2014), in Maharachchikumbura et al., Stud. Mycol. 79:147 (2014a) Neopestalotiopsis is an important plant pathogenic, saprobic and endophytic genus commonly present in tropical and subtropical ecosystems. The genus was introduced by Maharachchikumbura et al. (2014b). Species of Neopestalotiopsis are appendage-bearing asexual coelomycetes in the family Sporocadaceae (Jayawardena et al. 2016). Classification—Sordariomycetes, Xylariomycetidae, Amphisphaeriales, Sporocadaceae Type species—Neopestalotiopsis protearum (Crous & L. Swart) Maharachch. et al., in Maharachchikumbura et al., Stud. Mycol. 79:147 (2014a) Distribution—Worldwide Disease symptoms—Canker, dieback, fruit rots, leaf spot Pathogenic Neopestalotiopsis are recorded in post-harvest fruit rots of grapes, trunk diseases in grapevine in China, India and France, leaf spot disease of grapevine in China and leaf blights in many plant species worldwide (Hyde et al. 2014; Jayawardena et al. 2015, 2016; Maharachchikumbura et al. 2017). Neopestalotiopsis species infect a variety of grapevine cultivars, causing diseases including grapevine dieback, fruit rot, postharvest disease and severe defoliation. Initial symptoms of fruit rot disease are mostly observed at the splits between the pedicel and the berry and at the wounds of the fruits and severely infected fruits become rotten and separate completely from the pedicel (Jayawardena et al. 2015). Neopestalotiopsis asiatica and N. javaensis are associated with grapevine trunk disease (Maharachchikumbura et al. 2017). Grapevine trunk diseases reduce the yield and quality of grapes, even leading to partial or total death of individual plants. Neopestalotiopsis clavispora and N. surinamensis cause guava scab (Solarte et al. 2018). Neopestalotiopsis ellipsospora causes leaf spot on sweet potatoes 123 Fungal Diversity Table 10 Details of Macrophomina and Sphaeropsis isolates used in the phylogenetic analyses Species Isolate/voucher no SSU ITS LSU tef1 TUB2 Barriopsis fusca CBS 174.26* EU673182 EU673330 DQ377857 EU673296 EU673109 Botryobambusa fusicoccum CBS 134113* JX646826 JX646792 JX646809 JX646857 N/A MFLUCC 11-0657 JX646827 JX646793 JX646810 JX646858 N/A CBS 133992* JX646825 JX646791 JX646808 JX646856 JX646841 MFLUCC 10-0051 JX646824 JX646790 JX646807 JX646855 JX646840 CBS 119047* EU673175 DQ299245 EU673244 EU017539 EU673107 Botryosphaeria agaves B. corticis ATCC 22927 EU673176 DQ299247 EU673245 EU673291 EU673108 CBS 115476 * EU673173 AY236949 AY928047 AY236898 AY236927 CBS 110302 EU673174 AY259092 EU673243 AY573218 EU673106 Cophinforma atrovirens MFLUCC 11-0425* JX646833 JX646800 JX646817 JX646865 JX646848 Dothiorella iberica MFLUCC 11-0655 CBS 115041* JX646834 EU673155 JX646801 AY573202 JX646818 AY928053 JX646866 AY573222 JX646849 EU673096 B. dothidea Diplodia allocellula CBS 113188 EU673156 AY573198 EU673230 EU673278 EU673097 CBS 130408* N/A JQ239397 JQ239410 JQ239384 JQ239378 CBS 130410 N/A JQ239399 JQ239412 JQ239386 JQ239380 CBS 132777* N/A JN693507 N/A JQ517317 JQ411459 UCROK 1429 N/A JQ411412 N/A JQ512121 JQ411443 CBS 115812* EU673193 AY639595 DQ377902 DQ103566 DQ458860 CBS 116355 EU673194 AY639594 EU673252 DQ103567 EU673126 CBS 134112* JX646830 JX646797 JX646814 JX646862 JX646845 MFLUCC 11-0656 JX646831 JX646798 JX646815 JX646863 JX646846 CBS 499.66 KF531818 KF531820 DQ377925 KF531798 KF531800 CBS 251.49 KF531817 KF531819 DQ377923 KF531797 KF531799 Neodeightonia subglobosa CBS 448.81* EU673202 EU673337 DQ377866 EU673306 EU673137 N. phoenicum CBS 122528* EU673205 EU673340 EU673261 EU673309 EU673116 Macrophomina phaseolina CBS 227.33 KF531823 KF531825 DQ377906 KF531804 KF531806 M. pseudophaseolina CBS 162.25 CPC 21422 KF531824 N/A KF531826 KF951792 DQ377905 N/A KF951996 KF952154 KF531805 KF952234 D. agrifolia Lasiodiplodia gonubiensis L. lignicola Neoscytalidium hyalinum Phaeobotryon mamane Oblongocollomyces variabilis Sphaeropsis citrigena S. eucalypticola CPC 21417* N/A KF951791 N/A KF952153 KF952233 CPC 21524 N/A KF951799 N/A KF952161 KF952240 CBS 122980* EU673184 EU673332 EU673248 EU673298 EU673121 CPC 12442 EU673185 EU673333 DQ377899 EU673299 EU673124 CMW 25420 N/A EU101313 N/A EU101358 N/A CMW 25421, CBS 121775 N/A EU101314 N/A EU101359 N/A CMW 25422, CBS 121776 N/A EU101326 N/A EU101371 N/A CMW 25423 N/A EU101327 N/A EU101372 N/A ICMP 16812* EU673180 EU673328 EU673246 EU673294 EU673140 ICMP 16818 EU673181 EU673329 EU673247 EU673295 EU673141 CBS 133993* JX646835 JX646802 JX646819 JX646867 JX646850 MFLUCC 11-0654 JX646836 JX646803 JX646820 JX646868 JX646851 S. porosa CBS 110496* EU673179 AY343379 DQ377894 AY343340 EU673130 S. visci CBS 110574 CBS 122526 * N/A N/A AY343378 EU673324 N/A N/A AY343339 EU673292 N/A N/A CBS 186.97 EU673178 EU673325 DQ377868 EU673293 EU673128 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold 123 Fungal Diversity Table 11 Details of the Neonectria isolates used in the phylogenetic analyses Species Isolates/voucher no ITS LSU TUB tef1 Neonectria austroradicicola PDD 46334 G.J.S. 83-154 EF607077 – – – N candida CBS 151 29 IMI 113894/MUCL 28083 AY677291 AY677333 DQ789863 DQ789723 N. coccinea CBS 119158/GJS 98-114 JF268759 KC660620 KC660727 JF268734 N. confusa CBS 127485/HMAS 99197* FJ560437 KM515934 FJ860054 – N. confusa CBS 127484/HMAS 99198 KM515889 KM515933 KM515886 – N. ditissima CBS 100318 KM515890 KM515935 DQ789858 KM515944 N. ditissima CBS 100317 KM515891 KM515936 KM515887 KM515945 N. ditissimopsis HMAS 98329* JF268764 – JF268729 JF268745 N. faginata CBS 217.67/IMI 105738/ATCC 16547* HQ840385 HQ840382 JF268730 JF268746 N. faginata CBS 119160/GJS 04-159 HQ840384 HQ840383 DQ789883 DQ789740 N. fuckeliana N. hederae CBS 239.29/IMI 039700 IMI 058770a/ATCC 16543* HQ840386 – HQ840377 KC660617 DQ789871 DQ789895 JF268748 DQ789752 N. hederae CBS 714.97/PD 97/1932 – KC660616 DQ789878 KC660461 N. lugdunensis CBS 125485/DAOM 235831/TG 2008-07 KM231762 KM231625 KM232019 KM231887 N. major CBS 240.29/IMI 113909* JF735308 KM515942 DQ789872 JF735782 N. microconidia HMAS 98294 KC660530 KC660587 – – N. neomacrospora CBS 198.62/BBA 9628/IMI 113890 AJ009255 HM364316 HM352865 HM364351 N. neomacrospora CBS 324.61/DSM 62489/IMB 9628 JF735312 HM364318 DQ789875 – N. obtusispora CBS 183.36/IMI 113895 AM419061 KM515943 AM419085 JF735796 N. punicea CBS 242.29 KC660522 KC660565 DQ789873 DQ789730 N. shennongjiana HMAS 183185 FJ560440 – FJ860057 – N. tsugae CBS 788.69* KM231763 HQ232146 KM232020 – Thelonectria gongylodes CBS 12511/GJS 90-48 JQ403330 JQ403369 HM352870 HM364357 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold (Maharachchikumbura et al. 2016). Neopestalotiopsis clavispora causes crown and root rot of strawberry worldwide while N. iranensis infects leaves and fruits of strawberry (Ayoubi and Soleimani 2016), with the pathogen initially developing circular, black, and slightly sunken spots that expand outwards on the surface. Droplets of spores are scattered over the white aerial mycelial area and later cause soft decay of the fruit flesh (Ayoubi and Soleimani 2016). Canker and dieback on blueberry in Chile and Uruguay are also caused by N. clavispora (Espinoza et al. 2008; González et al. 2012; Chamorro et al. 2016). Neopestalotiopsis samarangensis has been described from wax apple fruit rot in Thailand (Maharachchikumbura et al. 2013a, b). In fruit rots, the initial symptom is small, circular, black, slightly sunken spots on fruits. Later, the spots enlarged rapidly, become sunken and result in a soft decay of the fruit flesh (Maharachchikumbura et al. 2013a, b). Hosts—Species of Fragaria 9 ananassa, Ipomoea, Malus, Psidium, Vaccinium and Vitis Morphological based identification and diversity Neopestalotiopsis species can be differentiated using morphology and molecular phylogeny (Maharachchikumbura et al. 2014b). There are 36 species epithets listed in Index Fungorum (2019). Neopestalotiopsis species differ from Pestalotiopsis and Pseudopestalotiopsis in having somewhat versicolorous median cells (Maharachchikumbura et al. 2014b) whereas both Pestalotiopsis and Pseudopestalotiopsis have concolourous median cells (Maharachchikumbura et al. 2014b) as well as its conidiophores which are indistinct and often reduced to conidiogenous cells (Maharachchikumbura et al. 2014b). Conidial morphology is widely used in taxonomy in pestalotioid fungi (Steyaert 1949; Guba 1961; Nag Raj 1993; Maharachchikumbura et al. 2012, 2014b). Species delimitation based on morphological characters is limited as these characters are plastic and vary between hosts and environments (Maharachchikumbura et al. 2011, 2016). Therefore, phylogenetic species recognition is an effective method to identify different pestalotioid species (Maharachchikumbura et al. 2016). Molecular based identification and diversity Neopestalotiopsis species can be roughly separated from Pestalotiopsis and Pseudopestalotiopsis based on the total number of base pairs in the ITS region 123 Fungal Diversity Fig. 17 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, LSU, tef1 and TUB sequence data of Neonectria species. Related sequences were obtained from GenBank. Twentythree strains are included in the analyses, which comprise 2336 characters including gaps. Tree topology of the ML analysis was similar to the one generated from BI (figure not shown). The best scoring RAxML tree with a final likelihood value of - 7942.756270 is presented. The matrix had 525 distinct alignment patterns, with 18.13% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.223071, C = 0.285136, G = 0.261197, T = 0.230596; substitution rates AC = 1.213729, AG = 2.500008, AT = 1.727890, CG = 0.720430, CT = 6.191594, GT = 1.000000; gamma distribution shape parameter a = 0.749195. Maximum likelihood bootstrap support (C 55%) and posterior probabilities (BYPP C 0.90) from Bayesian inference analysis are indicated respectively near the nodes. Ex-type strains are in bold. The tree is rooted in Thelonectria gongylodes (Maharachchikumbura et al. 2014b). However, the use of ITS sequences alone does not resolve Neopestalotiopsis species (Maharachchikumbura et al. 2012). Therefore, Maharachchikumbura et al. (2014b) suggested using combined ITS, TUB2 and tef1 genes to provide a better resolution in phylogenetic analyses. This study reconstructs the phylogeny of Neopestalotiopsis based on a combined ITS, TUB2 and tef1 sequence data (Fig 18, Table 12) and reveals similar phylogenetic relationships to previous studies by Maharachchikumbura et al. (2014b, 2016). Schröter (1886), but no species was assigned as a type for the genus (Constantinescu et al. 2005). Plasmopara nivea is considered as the type species of this genus (Constantinescu et al. 2005). Plasmopara species are commonly known as downy mildew pathogens. There are 2064 records in USDA fungal database under genus Plasmopara (Farr and Rosman 2019). Downy mildew has become one of the most troublesome diseases in agriculture including P. viticola on grape, P. geranii on geranium and P. halstedii on sunflower (McTaggart et al. 2015). Kamoun et al. (2015) categorized P. viticola among the top ten Oomycetes pathogens in plant pathology. Current interest in this genus is to understand the co-evolution with the host and effective disease management (Thines and Kamoun 2010). Taxonomically useful morphological or ecological characters are few for the downy mildews and this makes identification of synapomorphic states impossible (Göker et al. 2003). Classification—Oomycota incertae sedis, Peronosporea, Peronosporidae, Peronosporales, Peronosporaceae Type species—Plasmopara nivea (Unger) J. Schröt. Distribution—Worldwide Disease symptoms—Downy mildew Hosts—Species belonging to this genus are obligate biotrophs on a wide range of hosts including Acanthaceae, Asteraceae, Balsaminaceae, Geraniaceae, Malvaceae, Onagraceae, Orobanchaceae, Violaceae and Vitaceae Recommended genetic marker (genus level)—LSU Recommended genetic markers (Species level)—ITS, TUB2 and tef1 Accepted number of species: 41 species. References: Maharachchukumbura 2012, 2014b (morphology, phylogeny); Maharachchukumbura et al. 2016 (morphology, phylogeny); Jayawardena et al. 2015, 2016 (morphology, phylogeny, pathogenicity) Plasmopara J. Schröt., in Cohn, Krypt.-Fl. Schlesien 3.1(9–16): 236 (1886) [1889] The genus Plasmopara belongs to the family Peronosporaceae of the Peronosporales in Oomycetes (Riethmüller et al. 2002; Görg et al. 2017). This genus is included in this study as it is an important plant pathogen on many economically important crops. Plasmopara was introduced by 123 Fungal Diversity Fig. 18 Phylogram generated from maximum likelihood analysis based on combined ITS, TUB2 and tef1 sequence data of Neopestalotiopsis species. Related sequences were obtained from GenBank. Forty-three strains are included in the combined sequence analyses, which comprise 1391 characters with gaps. Pestalotiopsis diversiseta (MFLUCC 12-0287) is used as the outgroup taxa. The best scoring RAxML tree with a final likelihood value of - 5457.035085 is presented. The matrix had 409 distinct alignment patterns, with 6.30% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.231067, C = 0.270889, G = 0.213946, T = 0.284098; substitution rates AC = 0.847461, AG = 2.876343, AT = 1.282349, CG = 0.723831, CT = 3.850003, GT = 1.000000; gamma distribution shape parameter a = 0.235476. The maximum parsimonious dataset consisted of 1026 constant, 177 parsimonyinformative and 188 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 650 steps (CI = 0.688, RI = 0.609, RC = 0.419, HI = 0.312) in the first tree. RAxML and maximum parsimony bootstrap support value C 50% and posterior probabilities BYPP C 0.90 from Bayesian inference analysis are indicated respectively near the nodes, are shown respectively near the nodes. Ex-type strains are in bold (Voglmayr et al. 2004; Thines and Kamoun 2010; McTaggart et al. 2015). discussion of nomenclatural and taxonomic problems of this genus, Plasmopara was segregated in two different groups by morphology and phylogeny (Constantinescu et al. 2005). Constantinescu et al. (2005) proposed to introduce a new generic name for P. pygmaea and for six Morphological based identification and diversity Wilson (1907) was the first to consider P. pygmaea as the type of Plasmopara. However, even after a century of 123 Fungal Diversity Table 12 Details of the Neopestalotiopsis isolates used in the phylogenetic analyses Species Isolate no ITS TUB2 tef1 Neopestalotiopsis acrostichum MFLUCC 17-1754* MK764272 MK764338 MK764316 N. alapicalis MFLUCC 17-2544* MK357772 MK463545 MK463547 N. aotearoa MFLUCC 17-1754 MK764272 MK764338 MK764316 N. asiatica MFLUCC12-0286* JX398983 JX399018 JX399049 N. australis CBS 114159* KM199348 KM199432 KM199537 N. brachiata MFLUCC 17-1555* MK764274 MK764340 MK764318 N. chrysea MFLUCC12-0261* JX398985 JX399020 JX399051 N. clavispora MFLUCC 12-0281* JX398979 JX399014 JX399045 N. cocoes MFLUCC 15-0152* KX789687 – KX789689 N. coffeae-arabicae HGUP 4019* KF412647 – – N. cubana CBS 600 96* KM199347 KM199438 KM199521 N. egyptiaca CBS 140162* KP943747 KP943746 KP943748 N. ellipsospora MFLUCC 12-0283* JX398980 JX399016 JX399047 N. eucalypticola CBS 264 37* KM199376 KM199431 KM199551 N. foedans N. formicarum CGMCC3 9123* CBS 362 72* JX398987 KM199358 JX399022 KM199455 JX399053 KM199517 N. honoluluana CBS 114495* KM199364 KM199457 KM199548 N. iraniensis CBS 137768* KM074048 KM074057 KM074051 N. javaensis CBS 257 31* KM199357 KM199437 KM199543 N. keteleeria MFLUCC 13-0915* KJ503820 KJ503821 KJ503822 N. macadamiae BRIP 63738B* KX186604 KX186654 KX186627‘ N. magna MFLUCC12-652* KF582795 KF582793 KF582791 N. mesopotamica CBS 336 86* KM199362 KM199441 KM199555 N. musae MFLUCC 15-0776* KX789683 KX789686 KX789685 N. natalensis CBS 138 41* KM199377 KM199466 KM199552 N. pernambucana GS-2014 strain RV01* KJ792466 – KU306739 N. petila MFLUCC 17-1738* MK764275 MK764341 MK764319 N. piceana CBS 394 48* KM199368 KM199453 KM199527 N. protearum CBS 114178* JN712498 KM199463 KM199542 N. rhisophorae MFLUCC 17-1550* MK764277 MK764343 MK764321 N. rosae N. rosicola CBS 101057* CFCC 51992 KM199359 KY885239 KM199429 KY885245 KM199523 KY885243 N. samarangensis MFLUCC 12-0233* JQ968609 JQ968610 JQ968611 N. saprophytica MFLUCC 12-0282* KM199345 KM199433 KM199538 N. sonneratae MLFUCC 17-1745* MK764279 MK264345 MK264323 N. steyaertii IMI192475* KF582796 KF582794 KF582792 N. surinamensis CBS 450.74* KM199351 KM199465 KM199518 N. thailandica MFLUCC 17-1730* MK764281 MK764347 MK754325 N. umbrinospora MFLUCC 12-0285* JX398984 JX399019 JX399050 N. vitis MFLUCC 15-1265* KU140694 KU140685 KU140676 N. zimbabwana CBS 111495* – KM199456 KM199545 Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold other related species and they have established the current classification for Plasmopara. 123 Species belonging to Plasmopara have the following characters. Hyphae are intercellular, haustoria are intracellular, as obpyriform, globose, or slightly elongated Fungal Diversity vesicles (Göker et al. 2003; Voglmayr et al. 2004; Constantinescu et al. 2005). A callose sheath often surrounds haustoria. Sporangiophores are mostly present on the under leaf surface of the host, but sometimes also on other parts of the plant (eg. P. viticola produces sporangiophores on inflorescences and young berries, Zhang et al. 2017). Sporangiophores are colourless, branched in the upper part. They branch monopodially, in two to more orders (Göker et al. 2003; Constantinescu et al. 2005). Branches are more or less divergent, ending in a number of elongated ultimate branchlets. The newly formed wall closing the tip after sporangium discharge (Constantinescu et al. 2005). Callose plugs usually present in trunk and/or branches. Sporangiogenesis is holoblastic. These species produce sporangia synchronously, which vary in shape, sporangia wall is colourless, appearing smooth in light microscopy but showing various types of ornamentations in the electron microscope (Constantinescu et al. 2005). There are 199 epithets listed in Index Fungorum (2019), however, 40 of them do not belong to Plasmopara based on phylogenetic evidence (Figs. 19, 20). Oospores develop a single germ tube, terminating with sporangium, once a sporangium disseminated, by rain flash or wind, it releases zoospores (Ash 2000; Rossi et al. 2008; Carisse 2016; Kamoun et al. 2015; Wilcox et al. 2015). Molecular based identification and diversity Molecular and phylogenetic studies have shown that Plasmopara is polyphyletic (Riethmüller et al. 2002; Göker et al. 2003, 2007; Voglmayr et al. 2004; Voglmayr and Constantinescu 2008). Even though Wilson (1907) proposed P. pygmaea as the type species of the genus Plasmopara, it has a close relationship with Bremia, Paraperonospora and Basidiophora (Göker et al. 2003). With these morphological and phylogenetic aspects, many species that are traditionally included in Plasmopara have moved into new genera. The newly introduced genera are Viennotia (Göker et al. 2003), Protobremia (Voglmayr et al. 2004), and Plasmoverna (Constantinescu et al. 2005). Constantinescu et al. (2005) resolved Plasmopara phylogeny, introducing Plasmoverna as a new genus to accommodate the morphologically dissimilar and polyphyletic taxa belonging to previous classifications. Voglmayr and Constantinescu (2008) re-classified three species of Plasmopara into new genus Novotelnova Voglmayr & Constant. The species belonging to Novotelnova were identical in the analyses of the nuLSU and nuSSU-ITS15.8S datasets. Therefore, in the present study, we follow Voglmayr and Constantinescu (2008) to provide a backbone tree for Plasmopara using combined nuLSU sequence data (Fig. 21, Table 13). The downy mildew pathogens have been studied extensively to understand their host specificity and co- evolution with the host plants. The grape downy mildew has been identified as a host-specific cryptic species (Rouxel et al 2013; Zhang et al. 2017). Rouxel et al. (2013) considered the cryptic species as formae speciales: P. viticola f. sp. riparia (lineage A occurring on V. riparia and some hybrids); P. viticola f. sp. aestivalis (lineage B found on V. aestivalis, V. labrusca, V. vinifera and some hybrids); P. viticola f. sp. vinifera (lineage C occurring on V. vinifera and some hybrids); P. viticola f. sp. quinquefolia (lineage D found on V. quinquefolia). To understand the cryptic lineages genealogical concordance phylogenetic species recognition (GCPSR) approach is currently accepted (Taylor et al. 2000; Rouxel et al. 2013). GCPSR facilitate the most convenient analysis for species that cannot be cultivated or mate in control conditions (O’Donnell et al. 2000; Steenkamp et al. 2002; Rouxel et al. 2013). Recommended genetic marker (genus level)—LSU Recommended genetic marker (species level)—LSU The universal barcode for the Oomycetes, the cytochrome oxidase subunit 1 and 2 genes (cox 1 and cox 2) are used. However Choi et al. (2015) suggested cox2 is better suited to this because of its ease of amplification among oomycete lineages, better performance on herbarium specimens, higher discriminatory power at the species level and the availability of a large taxonomically diverse database that already includes many species of oomycetes, especially the downy mildew. In previous studies, nuLSU gene regions (D1–D3 and D7–D8 sequences) were widely used (Riethmüller et al. 2002; Göker et al. 2003, 2007; Voglmayr et al. 2004; Voglmayr and Constantinescu 2008). Branch supports of the backbone tree was often higher in the nuLSU data, which resulted in a larger data matrix and a higher number of parsimony-informative characters than when ITS was used (Voglmayr and Constantinescu 2008). No study has combined these gene regions or any other gene regions as the marker to understand the phylogenetic relationship within the genus. Accepted number of species: There are 199 species in Index Fungorum (2019) and only 19 species have molecular data in this genus. References: Riethmüller et al. 2002; Göker et al. 2003; 2007; Voglmayr et al. 2004; Voglmayr and Constantinescu 2008; Rouxel et al 2013; Zhang et al. 2017 (morphology, phylogeny). Pseudopestalotiopsis Maharachch., K.D. Hyde & Crous (2014), in Marachchikumbura et al., in Maharachchikumbura et al., Stud. Mycol. 79:180 (2014a) The genus was introduced by Maharachchikumbura et al. (2014b) with Pseudopestalotiopsis theae (Sawada) Maharachch., K.D. Hyde & Crous as the type species. Species of Pseudopestalotiopsis are appendage-bearing phenotypically diverse coelomycetes in the family 123 Fungal Diversity Fig. 19 Grape downy mildew disease symptoms. a Infected grapevines, b–c appearance of oil spot on the upper leaf surface. d Sporulation on the lower leaf surface. e Young infected berries with sporulation. f Infection on fruits Sporocadaceae and are commonly found in tropical and subtropical ecosystems (Jaklitsch et al. 2016; Maharachchikumbura et al. 2016). Pseudopestalotiopsis is characterized by brown to dark brown or olivaceous median cells and knobbed or not knobbed apical appendages (Maharachchikumbura et al. 2014b, 2016). The epitype of Pseudopestalotiopsis theae (Sawada) Steyaert was designated from fresh leaves of Camellia sinensis collected in Thailand (Maharachchikumbura et al. 2013a, b). Pseudopestalotiopsis has been studied for the production of various secondary metabolites with diverse structural features, with antitumour, antifungal, antimicrobial and other activities (Ding et al. 2008; Maharachchikumbura et al. 2011, 2016). Pseudopestalotiopsis theae is economically significant as it has been identified as a pathogen in major tea-growing areas in the world (Maharachchikumbura et al. 2016). Pseudopestalotiopsis theae causes grey blight of tea and reduces yield (Maharachchikumbura et al. 2011, 2013a, b, 2016). Pseudopestalotiopsis theae was also isolated as an endophyte from different hosts (Camellia nitidissima, C. sinensis, Holarrhena antidysenterica, Podocarpus macrophyllus, Terminalia arjuna) or as a saprobe (seeds of Diospyros crassiflora) (Maharachchikumbura et al. 2011, 2013a, b, 2016). 123 Classification—Sordariomycetes, Xylariomycetidae, Amphisphaeriales, Sporocadaceae Type species—Pseudopestalotiopsis theae (Sawada) Maharachch., in Maharachchikumbura et al., Stud. Mycol. 79:183 (2014a) Distribution—China, India, Indonesia, Malaysia, Thailand (Maharachchikumbura et al. 2016) Disease symptoms—Pseudopestalotiopsis theae causes grey blight in major tea growing areas in the world (Horikawa 1986, Maharachchikumbura et al. 2013a, b, 2016). The pathogen develops circular to irregular leaf spots initially and grey, brown margins when mature, covering up to half of the leaf with acervuli (Maharachchikumbura et al. 2016). Pseudopestalotiopsis ixorae and P. taiwanensis cause a leaf spot which initially develops small, circular, ash-coloured spots which later turn into brown spots (Tsai et al. 2018). Hosts—Averrhoa carambola, Camellia sp., Cinnamomum sp., Cocos nucifera, Diospyros crassiflora, Fragaria sp., Hibiscus rosa-sinensis, Holarrhena antidysenterica, Ixora sp., Kandelia obovate, Macaranga sp., Pandanus odoratissimus, Podocarpus macrophyllus, Prunus sp., Terminalia arjuna and Thea sinensis Fungal Diversity Fig. 20 Disease cycle of grape downy mildew. Redrawn from Kassemeyer (2017) Morphological based identification and diversity Molecular based identification and diversity Pseudopestalotiopsis can be distinguished from Neopestalotiopsis and Pestalotiopsis by dark concolourous median cells with indistinct conidiophores (Maharachchikumbura et al. 2014b, 2016). However, there could be a wide host range for Pseudopestalotiopsis species and the actual number of species could be much higher than presently known (Maharachchikumbura et al. 2011, 2016). Conidial morphology is widely used in taxonomy in pestalotioid fungi (Steyaert 1949; Guba 1961; Nag Raj 1993; Maharachchikumbura et al. 2011, 2012, 2014b). Species delimitation based on morphological characters is limited as these characters are plastic and vary between hosts and environments (Maharachchikumbura et al. 2011, 2016). Therefore, phylogenetic species recognition is an effective method to identify different pestalotioid species (Maharachchikumbura et al. 2016). ITS sequence data alone is not sufficient for species delimitation of Pseudopestalotiopsis. Therefore, Maharachchikumbura et al. (2012) suggested a phylogenetic analysis of combined ITS, TUB2 and tef1 genes provide better resolution as compared to single gene phylogeny (Fig. 22, Table 14). Recommended genetic markers (genus level)—LSU (as outlined in Maharachchikumbura et al. 2012) Recommended genetic markers (species level)—ITS, TUB2 and tef1 (as outlined in Maharachchikumbura et al. 2012) Accepted number of species: 20 species References: Maharachchukumbura 2013a, b, 2014b, 2016b (morphology, phylogeny) Rosellinia De Not., G. bot. ital.1 (1): 334(1844) Rosellinia (Xylariaceae) species are characterized mainly as saprobes, some endophytes and occasionally as pathogens. They have a worldwide distribution and common in both temperate and tropical regions (Petrini 123 Fungal Diversity Fig. 21 Phylogenetic tree generated by maximum parsimony analysis of LSU sequence data of Plasmopara species. Related sequences were obtained from GenBank. Nineteen strains are included in the analyses, which comprise 1263 characters including gaps. The tree was rooted with Phytophthora arece (AR 234). Tree topology of the MP analysis was similar to the ML. The maximum parsimonious dataset consisted of constant 1053, 110 parsimony-informative and 100 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of two equally most parsimonious trees with a length of 365 steps (CI = 0.641, RI = 0.539, RC = 0.345, HI = 0.359) in the first tree. The best scoring RAxML tree with a final likelihood value of - 3660.849005 is presented. The matrix had 254 distinct alignment patterns, with 30.91% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.229156, C = 0.177763, G = 0.308486, T = 0.284595; substitution rates AC = 0.706031, AG = 4.368078, AT = 1.048734, CG = 0.141039, CT = 7.063364, GT = 1.000000; gamma distribution shape parameter a = 0.163551. RAxML and maximum parsimony bootstrap support value C 50% (BT) are shown respectively near the nodes 1993, 2013; ten Hoopen and Krauss 2006). Plant pathogenic Rosellinia species play a vital role in economically important crops, trees and ornamental plants. Rosellinia desmazieresii and R. necatrix are mostly known from temperate regions, while R. bunodes is known only from the tropics causing root rot on fruit trees and vines (Agrios 2005; ten Hoopen and Krauss 2006). Among the root diseases cause by Rosellinia species, R. bunodes is responsible for black root rot, R. necatrix for white root rot and R. pepo for stellate root rot (Castro et al. 2013). Species of this genus can survive as microslerotia in wood, roots and soil and the infection spreads through feeder roots when they contact hyphae or microsclerotia (Ploetz et al. 2003). 123 Fungal Diversity Table 13 Details of the Plasmopara isolates used in the phylogenetic tree Species Isolate/voucher no Host LSU Plasmopara australis HV 2867 Luffa cylindrica KT159461 P. baudysii HV 571 Berula erecta AY035517 P. densa HV 2232 Rhinanthus minor EF553463 P. epilobii HV988 Epilobium parviflorum AY250178 P. euphrasiae EV 301 Euphrasia rostkoviana EF553467 P. geranii PA5 Geranium maculatum DQ148397 P. geranii-sylvatici HV411 Geranium sylvaticum DQ148398 P. halstedii RDM TC14 Rudbeckia fulgida KP164999 P. laserpitii HV2051 Laserpitium latifolium KC495034 P. mei-foeniculi AR284 Meum athamanticum AY250160 P. pastinacae HV1090 Pastinaca sativa AY250157 P. peucedani AR277 Peucedanum palustre AY250154 P. praetermissa HV2061 Geranium sylvaticum DQ148396 P. skvortzovii AR306 Abutilon theophrasti AY250179 P. solidaginis P. sphagneticolae R409 BRIP Solidago virgaurea Sphagneticola trilobata AY250144 KM085176 P. viticola AR 160 Vitis vinifera AY035524 P. wildemaniana AR324 Hypoestes sp. AY250180 P. wilsonii HV2065 Geranium nepalense DQ148408 Phytophthora arecae AR 243 Unknown AY035530 Rosellinia was introduced to accommodate species which are characterized by uniascomatal and carbonaceous stromata that develop within a subiculum. There have been different contradiction placements of Rosellinia. Miller (1928) placed it in the family Xylariaceae and this was confirmed in morphology and phylogeny-based studies later (Hsieh et al. 2010; Daranagama et al. 2015). Daranagama et al. (2018) and Wendt et al. (2018) revealed that Rosellinia is closely related to Entoleuca and Nemania. Classification—Sordariomycetes, Xylariomycetidae, Xylariales, Xylariaceae Type species—Rosellinia aquila (Fr.) Ces. & De Not., G. bot. ital.1 (1): 334(1844) Distribution—Worldwide Disease symptoms—Root rots Black root rot is characterized by the occurrence in patches that extend in a circular pattern. Rosellinia bunodes the main causal agent of black root rot typically shows black branching strands that are firmly attached to the roots and may form condensed irregular knots and chlorotic leaves may shed gradually (Sivanesan and Holiday 1972; Oliverira et al. 2008). The symptoms of white root rot caused by R. necatrix in the upper parts of the plants (such as yellow foliage, shrivelled fruits, no new growth) cannot be recognized in early stages of root infection. Cottony, white mycelia cover feeder roots of a tree and decay sets in. Mycelia grow into the soil and upward in the tree forming small, pale patches under or in the bark of major roots, root crown and lower trunk which eventually decay. A purple canker in wood at the root crown of young trees can also be caused by the fungus. Diseased trees will defoliate and premature death may occur (Pérez-Jiménez 2006; Pasini et al. 2016). Hosts—This genus has a wide range of hosts including Adoxaceae, Annonaceae, Apiaceae, Asteraceae, Betulaceae, Celastraceae, Convolvulaceae, Euphorbiaceae, Fabaceae, Fagaceae, Grossulariaceae, Juglandaceae, Lauraceae, Moraceae, Myrtaceae, Oleaceae, Pinaceae, Poaceae, Rosaceae, Rutaceae, Salicaceae, Sapindaceae, Scrophulariaceae, Tamaricaceae, Verbenaceae, Vitaceae and Zingiberaceae. Morphological based identification and diversity The genus is characterized by globose-subglobose, uni- to multiloculate, often collapsed ascomata, mostly detached from the stroma wall,; septate, hyaline paraphyses, asci that are 8-spored, unitunicate, cylindrical to clavate, long pedicellate, rounded at the apex, with J ? apical ring bluing in Melzer’s reagent, massive barrel-shaped with distinctive rings ascospores that are uniseriate, unicellular, elongated ellipsoidal-fusiform, light to dark brown, with germ slits, cellular appendages and/or may be slimy sheaths or caps and a dematophora-like or geniculosporium-like asexual morphs (Daranagama et al. 2018). Rosellinia is a large genus with 483 epithets in Mycobank, 517 in Index Fungorum and 311 in Global Biodiversity Information Facility (GBIF); there are currently 158 accepted species (Petrini 2013; Li and Guo 2015; Li et al. 123 Fungal Diversity Fig. 22 Phylogram generated from maximum likelihood analysis based on combined ITS, TUB2 and tef1 sequence data of Pseudopestalotiopsis species. Related sequences were obtained from GenBank. Twenty-five strains are included in the combined sequence analyses, which comprise 1404 characters with gaps. Neopestalotiopsis natalensis (CBS 138.41) was used as the outgroup taxa. The best scoring RAxML tree with a final likelihood value of - 4028.799660 is presented. The matrix had 274 distinct alignment patterns, with 6.34% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.235765, C = 0.270775, G = 0.213073, T = 0.280387; substitution rates AC = 1.242401, AG = 3.217138, AT = 1.272343, CG = 0.837226, CT = 4.463116, GT = 1.000000; gamma distribution shape parameter a = 0.229606. The maximum parsimonious dataset consisted of 1122 constant, 79 parsimonyinformative and 203 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of four equally most parsimonious trees with a length of 386 steps (CI = 0.832, RI = 0.737, RC = 0.613, HI = 0.168) in the first tree. RAxML and maximum parsimony bootstrap support value C 50% are shown respectively near the nodes. Bayesian posterior probabilities C 0.95 (BYPP) indicated as thickened black branches. Ex-type strains are in bold 2015, 2016; Su et al. 2016; Crous et al. 2017; Fournier et al. 2017a, b; Tibpromma et al. 2017). Petrini (2013) found seven morphologically distinct groups with distinguishing morphological characters associated with the shape, size and orientations of stroma, ostiole, ascospores and germ slit, which can be used for species delimitation (Fig. 23). Molecular based identification and diversity 123 Protein coding gene sequences are available for nine species of Rosellinia, mostly with only ITS and LSU sequence data. However, with the limited data, Daranagama et al. (2018) provided an updated backbone tree for genera in Xylariaceae, and Rossellinia clustered with Nemania and Entoleuca. Several phylogenetic studies have focused on Fungal Diversity Table 14 Details of the Pseudopestalotiopsis isolates used in the phylogenetic analyses Species Isolates ITS TUB2 tef1 Pseudopestalotiopsis ampullacea LC6618* KX895025 KX895358 KX895244 P. avucenniae MFLUCC 17-0434* MK764287 MK764353 MK764331 P. camelliae-sinensis LC3490* KX894985 KX895316 KX895202 P. chinensis LC3011* KX894937 KX895269 KX895154 P. cocos CBS 272.29* KM199378 KM199467 KM199553 P. dawaina MM14-F0015* LC324750 LC324751 LC324752 P. curvatispora MFLUCC 17-1722* MK764288 MK764354 MK764332 P. ignota NN 42909* KU500020 – KU500016 P. indica CBS 459.78* KM199381 KM199470 KM199560 P. ixorae NTUCC 17-001.1* MG816316 MG816326 MG816336. P. jiangxiensis LC 4479* KX895034 KX895343 KX895229 P. kawthaungina MM14-F0083 LC324753 LC324754 LC324755 P. kubahensis UMAS KUB-P20* KT006749 – – P. myanmarina NBRC 112264* LC114025 LC114045 LC114065 P. rhizophorae P. smitheae MFLUCC 17-1560* MFLUCC 12-0121* MK764291 KJ503812 MK764357 KJ503815 MK764335 KJ503818 P. thailandica MFLUCC 17-1724* MK764292 MK764358 MK764336 P. taiwanensis NTUCC 17-002.1* MG816319 MG816329 MG816339 P. theae MFLUCC 12-0055* JQ683727 JQ683711 JQ683743 P. vietnamensis NBRC 112252* LC114034 LC114054 LC114074 Ex-type (ex-epitype) strains are in bold and marked with an asterisk* and voucher stains are in bold pathogenic species such as R. bunodes and R. pepo. Castro et al. (2013) investigated R. bunodes and R. pepo isolated from Coffea arabica (Rubiaceae), Hevea brasiliensis (Euphorbiaceae), Macadamia integrifolia (Proteaceae), Psidium guajava (Myrtaceae) and Theobroma cacao (Malvaceae) using ITS based phylogenetic analyses from Colombia. Another ITS-based phylogenetic study identified R. necatrix, the pathogen responsible for white root disease on Aronia melanocarpa (Rosaceae) in Korea (Choi et al. 2017). This study reconstructs the phylogeny of Rosellinia based on analyses of combined ITS, LSU and RPB2 sequence data (Table 7, Fig. 13). The phylogenetic tree is updated with recently introduced Rosellinia species and corresponds to previous studies (Li et al. 2015, 2016; Su et al. 2016; Crous et al. 2017; Fournier et al. 2017a, b; Tibpromma et al. 2017). Recommended genetic markers (genus level)—LSU, ITS Recommended genetic marker (species level)—ITS Based on several studies and the availability of sequence data, ITS based phylogenetic studies are sufficient to identify Rosellinia to species level. There are few other studies carried out using LSU, ITS and RPB2 sequences. With a lack of sequence data for most species, there are some contradictions for the species and generic delimitat ion. Accepted number of species: 158 with only 26 species with molecular data References: Petrini 2013; Li and Guo 2015; (morphology), Castro et al. 2013; Li et al. 2015, 2016; Crous et al. 2017; Fournier et al. 2017a, b; Tibpromma et al. 2017, Daranagama et al. 2018 (morphology, phylogeny), Shimizu et al. 2012; dos Santos et al. 2017; Arjona-Girona and López-Herrera 2018; Kleina et al. 2018 (pathogenicity). Sphaeropsis Sacc., Michelia 2: 105. 1880. The genus Sphaeropsis was introduced by Saccardo (1880) (for species of Diplodia with brown, aseptate conidia), with S. visci as the type species. Sphaeropsis is the asexual morph of Phaeobotryosphaeria (Phillips et al. 2008, 2013; Wijayawardene et al. 2017). Species in Sphaeropsis seem to be cosmopolitan in distribution since they have been recorded from both temperate and tropical countries (i.e. Germany, New Zealand, South Africa, Thailand (Phillips et al. 2013; Slippers et al. 2014; Farr and Rossman 2019). Host specificity of Sphaeropsis has not yet been clarified and species have been recorded from various plant families. Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Sphaeropsis visci (Alb. & Schwein.) Sacc. Distribution—Worldwide Disease symptoms—calyx-end rot, stem end rot The decayed tissues in rot diseases are firm or spongy and brown in colour. The skin of decayed areas generally remains brown or dark brown but may appear dark in aged areas (Kim et al. 2005). 123 Fungal Diversity Fig. 23 Rosellinia bunodes (holotype, K(M) 62957, Sri Lanka, Peradeniya, on dead wood, November 1867, G.H.K. Thwaites) a, e Stromata (e ostiole white arrow). b–d Herbarium details. f Paraphyses. g–j Ascospores (g germ slit black arrow). Scale bars: e = 500 lm, g–j = 20 lm, f = 5 lm Hosts—Broad range of hosts, including Myrtaceae, Rutaceae, Santalaceae and Vitaceae. have been identified from culture. Sphaeropsis porosa differs from other species in having distinct pitted conidial walls. Sphaeropsis visci and S. citrigena can be distinguished from each other with their conidial pigmentation and swollen paraphyses tips (Phillips et al. 2013). Morphological based identification and diversity Over 600 species names are listed in Index Fungorum (2019), but few of them are currently in use and for most species cultures are not available except for S. citrigena (A.J.L. Phillips et al.) A.J.L. Phillips & A. Alves, S. eucalypti Berk. & Broome, S. porosa (Van Niekerk & Crous) A.J.L. Phillips & A. Alves, and S. visci (Alb. & Schwein.) Sacc. Pycnidial paraphyses in Sphaeropsis species distinguish this genus from Diplodia species, which do not have paraphyses. The aseptate, smooth-walled conidia of Sphaeropsis species differentiate them from Lasiodiplodia species, which have 1-septate, striate conidia. Recently, S. variabilis was transferred to a separate genus, Oblongocollomyces due to distinct morphological differences (Yang et al. 2017). Colony and conidial morphology are the primary characters to identify species within this genus (Ellis 1971, 1976; Simmons 1992). The sexual and asexual morphs connection of Sphaeropsis was established by Phillips et al. (2008) who obtained coelomycetes with large, brown, aseptate conidia typical of Sphaeropsis from Phaeobotryosphaeria culture. Four Sphaeropsis species 123 Molecular based identification and diversity Phillips et al. (2013) suggested that phylogenetic analysis of combined SSU, LSU, ITS, tef1 and TUB2 genes provide better resolution compared to ITS alone. This study provides the phylogenetic analyses of combined ITS, LSU, SSU, tef1 and TUB2 sequence data (Table 10, Fig. 16). The topology of the Sphaeropsis species tree is identical to the phylogeny tree of Phillips et al. (2013). Recommended genetic markers (genus level)—LSU and SSU Recommended genetic markers (species level)—ITS, tef1 and TUB2 Accepted number of species: There are 624 species epithets in Index Fungorum (2019) under this genus. However, only four species have sequence data. References: Phillips et al. 2013; Yang et al. 2017 (morphology, phylogeny). Fungal Diversity Updates on important phytopathogens Alternaria Nees, Syst. Pilze (Würzburg): 72 (1816) Species of Alternaria are saprotrophs on dead vegetation and are frequently isolated from soil, air, dust and waterdamaged buildings (Ellis 1971, 1976; De Hoog and Horré 2002; Runa et al. 2009; Woudenberg et al. 2013; Lawrence et al. 2016). The majority of species, however, are pathogens, infecting a vast array of host species (Jayawardena et al. 2019). A detailed background, diseases and the symptoms, morphological characters is discussed in Jayawardena et al. (2019). In this paper, we provide an update for the sections in Alternaria based on six gene combination analyses (Al Ghafri et al. 2019; Table 15, Fig. 24). Diplodia Fr., in Montagne, Annls Sci. Nat., Bot., sér. 2 1: 302 (1834) The genus Diplodia was introduced by Montagne (1834) and comprises species with hyaline or dark brown, aseptate or 1-septate, thick-walled conidia (Phillips et al. 2005). Diplodia is defined by having unilocular, solitary or aggregated conidiomata lined with conidiogenous cells that form conidia at their tips (Phillips et al. 2005). The type species of Diplodia is Diplodia mutila (Montagne 1834; Fries 1849), but there are no living cultures linked to the holotype of this species. As this has severely hampered studies on taxonomy and phylogeny of Diplodia, Alves et al. (2004) provided a detailed description of D. mutila based on an isolate from grapevines in Portugal (CBS 112553). Alves et al. (2014) designated an epitype for Diplodia mutila, with associated ex-epitype cultures. This epitype confirmed in all ways with the isotype of D. mutila and with the asexual morph on BPI 599153 as described by Alves et al. (2004). Diplodia mutila has hyaline conidia that become brown and one-septate after discharge from the pycnidia. Species of Diplodia can be differentiated on slight differences in conidial dimensions (Alves et al. 2014). Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Diplodia mutila (Fr. : Fr.) Fr., Summa Veg. Scand. 2:417 (1849) Distribution—Worldwide Disease symptoms—Diebacks, cankers, fruit rots. Hosts—Plurivorous on woody hosts. Morphological based identification and diversity Diplodia is a large genus and a search in MycoBank (2019) revealed 1398 names while Index Fungorum (2019) has 1268 names. Cryptic speciation is common in the genus, which makes species identification difficult if based only on morphological characters (Phillips et al. 2012, 2013). Dissanayake et al. (2016) included 26 Diplodia species in their phylogeny. Recently, a novel species Diplodia eriobotryicola on Eriobotrya japonica from Spain was introduced by González-Domı́nguez et al. (2016). Yang et al. (2017) introduced D. pyri on Pyrus sp., the Netherlands, D. citricarpa on Citrus sp., Iran, and D. gallae on galls of Quercus sp. However, the ITS and tef1 of the novel species, D. citricarpa are not available in GenBank and hence we could not include this species in our phylogeny. The genus now comprises 30 species known from culture. Molecular based identification and diversity Earlier taxonomic studies on Diplodia using molecular data employed ITS rDNA, but this single marker can underestimate species diversity among closely related or cryptic species. Multiple gene sequence concordance phylogenies have therefore been applied to identify cryptic or previously overlooked species of Diplodia (Slippers et al. 2004a, b, c; Burgess et al. 2006; Phillips et al. 2005, 2012, 2013; Hyde et al. 2014; Dissanayake et al. 2016). As the tef1 gene is considerably more variable than the ITS rDNA region in these taxa, data from tef1 have been combined with ITS sequence data. Unfortunately, no single gene region is sufficient to distinguish all species in this genus. The present phylogenetic analysis was performed based on up to date ex-holotype or ex-epitype sequence data available in GenBank (Fig. 25, Table 16). Recommended genetic markers (genus level)—SSU and LSU Recommended genetic markers (species level)—ITS, tef1, TUB2 Accepted number of species: 30 species References: Phillips et al. 2013 (morphology, phylogeny, distribution, hosts); Dissanayake et al. 2016 (phylogeny). Dothiorella Sacc., Michelia 2(6): 5 (1880) Dothiorella was proposed by Saccardo to accommodate D. pyrenophora (Hyde et al. 2014). Members of this genus are pathogens, endophytes and saprobes (Phillips et al. 2013; Dissanayake et al. 2016). Taxonomy of this genus has been in a state of flux for decades (Phillips et al. 2013). Sivanesan (1984) treated D. pyrenophora as a synonym of Dothichiza sorbi (asexual morph of Dothiora pyrenophora). However, Sivanesan (1984) was referring to Dothiorella pyrenophora Sacc. (1884) which, according to Sutton (1977), is a later homonym of Dothiorella pyrenophora Sacc. (1880). Crous and Palm (1999) studied the holotype of D. pyrenophora and considered it a synonym of Diplodia. However, Phillips et al. (2005) based on both morphological and molecular data revived the genus Dothiorella for species in which the conidia become brown and 1-septate while attached to the conidiogenous cells. 123 Fungal Diversity Table 15 Details of the Alternaria isolates used in the phylogenetic analyses Species name Strain number GenBank accession numbers SSU LSU RPB2 ITS GPDH tef1 KC584707 Alternaria abundans CBS 534.83 KC584581 KC584323 KC584448 JN383485 KC584154 A. alternantherae CBS 124392 KC584506 KC584251 KC584374 KC584179 KC584096 KC584633 A. alternariae CBS 126989 KC584604 KC584346 KC584470 AF229485 AY278815 KC584730 A. alternate CBS 916.96 KC584507 DQ678082 KC584375 AF347031 AY278808 KC584634 A. arborescens CBS 102605 KC584509 KC584253 KC584377 AF347033 AY278810 KC584636 A. argyranthemi CBS 116530 KC584510 KC584254 KC584378 KC584181 KC584098 KC584637 A. arrhenatheri A. aspera BMP 0514 CBS 115269 – KC584607 – KC584349 – KC584474 JQ693680 KC584242 JQ693629 KC584166 – KC584734 A. atra CBS 195.67 KC584608 KC584350 KC584475 AF229486 KC584167 KC584735 A. axiaeriisporifera CBS 118715 KC584513 KC584257 KC584381 KC584184 KC584101 KC584640 A. bornmueller DAOM 231361 KC584624 KC584366 KC584491 FJ357317 FJ357305 KC584751 A. botryospora CBS 478.90 KC584594 KC584336 KC584461 AY278844 AY278831 KC584720 A. botrytis CBS 197.67 KC584609 KC584351 KC584476 KC584243 KC584168 KC584736 A. brassicae CBS 116528 KC584514 KC584258 KC584382 KC584185 KC584102 KC584641 A. brassicae-pekinensis CBS 121493 KC584611 KC584353 KC584478 KC584244 KC584170 KC584738 A. brassicicola CBS 118699 KC584515 KC584259 KC584383 JX499031 KC584103 KC584642 A. breviramosa CBS 121331 KC584574 KC584318 KC584442 FJ839608 KC584148 KC584700 A. calycipyricola CBS 121545 KC584516 KC584260 KC584384 KC584186 KC584104 KC584643 A. capsici-annui CBS 504.74 C584517 KC584261 KC584385 KC584187 KC584105 KC584644 A. caricis CBS 480.90 KC584600 KC584342 KC584467 Y278839 AY278826 C584726 A. carotiincultae CBS 109381 KC584518 KC584262 KC584386 KC584188 KC584106 KC584645 A. cetera A. chartarum CBS 121340 CBS 200.67 KC584573 KC584614 KC584317 KC584356 KC584441 KC584481 JN383482 AF229488 AY562398 KC584172 KC584699 KC584741 A. cheiranthi CBS 109384 C584519 C584263 C584387 F229457 C584107 C584646 A. chlamydospora CBS 491.72 KC584520 KC584264 KC584388 KC584189 KC584108 KC584647 A. chlamydosporigena CBS 341.71 KC584584 KC584326 KC584451 KC584231 KC584156 KC584710 A. cinerariae CBS 116495 KC584521 KC584265 KC584389 KC584190 KC584109 KC584648 A. concatenate CBS 120006 KC584613 KC584355 KC584480 KC584246 AY762950 KC584740 A. conjuncta CBS 196.86 KC584522 KC584266 KC584390 J266475 Y562401 KC584649 A. conoidea CBS 132.89 KC584585 KC584327 KC584452 AF348226 FJ348227 KC584711 A. consortialis CBS 104.31 KC584615 KC584357 KC584482 KC584247 KC584173 KC584742 A. cucurbitae CBS 483.81 KC584616 KC584358 KC584483 FJ266483 AY562418 KC584743 A. cumini CBS 121329 KC584523 KC584267 KC584391 KC584191 KC584110 KC584650 A. daucifolii CBS 118812 KC584525 KC584269 KC584393 KC584193 KC584112 KC584652 A. dennisii CBS 110533 KC584586 KC584328 KC584453 KC584232 KC584157 KC584712 A. dennisii CBS 476.90 KC584587 KC584329 KC584454 JN383488 JN383469 KC584713 A. dianthicola CBS 116491 KC584526 KC584270 KC584394 KC584194 KC584113 KC584653 A. didymospora A. elegans CBS 766.79 CBS 109159 KC584588 KC584527 KC584330 KC584271 KC584455 KC584395 FJ357312 KC584195 FJ357300 KC584114 KC584714 KC584654 A. embellisia CBS 339.71 KC584582 KC584324 KC584449 KC584230 KC584155 KC584708 A. eryngii CBS 121339 KC584529 KC584273 KC584397 Q693661 Y562416 KC584656 A. eureka CBS 193.86 KC584589 KC584331 KC584456 JN383490 JN383471 KC584715 A. geniostomatis CBS 118701 KC584532 KC584276 KC584400 KC584198 KC584117 KC584659 A. gypsophilae CBS 107.41 KC584533 KC584277 KC584401 KC584199 KC584118 KC584660 A. helianthiinficiens CBS 117370 KC584534 KC584278 KC584402 KC584200 KC584119 KC584661 A. helianthiinficiens CBS 208.86 KC584535 KC584279 KC584403 JX101649 KC584120 EU130548 A. heterospora CBS 123376 KC584621 KC584363 KC584488 KC584248 KC584176 KC584748 123 Fungal Diversity Table 15 (continued) Species name Strain number GenBank accession numbers SSU LSU RPB2 ITS GPDH tef1 A. hyacinthi CBS 416.71 KC584590 KC584332 KC584457 KC584233 KC584158 KC584716 A. indefessa CBS 536.83 KC584591 KC584333 KC584458 KC584234 KC584159 KC584717 A. infectoria CBS 210.86 KC584536 KC584280 KC584404 DQ323697 AY278793 KC584662 A. japonica A. kulundii CBS 118390 M313 KC584537 KJ443087 KC584281 KJ443132 KC584405 KJ443176 KC584201 KJ443262 KC584121 KJ649618 KC584663 - A. leucanthemi CBS 421.65 KC584605 KC584347 KC584472 KC584240 KC584164 KC584732 A. leucanthemi CBS 422.65 KC584606 KC584348 KC584473 KC584241 KC584165 KC584733 A. limaciformis CBS 481.81 KC584539 KC584283 KC584407 KC584203 KC584123 KC584665 A. macrospora CBS 117228 KC584542 KC584286 KC584410 KC584204 KC584124 KC584668 A. nepalensis CBS 118700 KC584546 KC584290 KC584414 KC584207 KC584126 KC584672 A. nobilis CBS 116490 KC584547 KC584291 KC584415 KC584208 KC584127 KC584673 A. obclavata CBS 124120 KC584575 FJ839651 KC584443 KC584225 KC584149 KC584701 A. oudemansii CBS 114.07 KC584619 KC584361 KC584486 FJ266488 KC584175 KC584746 A. omaniana SQUCC 13580 MK878559 MK878556 MK880893 MK878562 MK880899 MK880896 A. omaniana SQUCC 15560 MK878560 MK878557 MK880894 MK878563 MK880900 MK880897 A. omaniana SQUCC 15561 MK878561 MK878558 MK880895 MK878564 MK880901 MK880898 A. panax CBS 482.81 KC584549 KC584293 KC584417 KC584209 KC584128 KC584675 A. papavericola CBS 116606 KC584579 KC584321 KC584446 FJ357310 FJ357298 KC584705 A. penicillata A. penicillata CBS 116608 116607 KC584572 KC584580 KC584316 KC584322 KC584440 KC584447 FJ357311 KC584229 FJ357299 KC584153 KC584698 KC584706 A. perpunctulata CBS 115267 KC584550 KC584294 KC584418 KC584210 KC584129 KC584676 A. petroselini CBS 112.41 KC584551 KC584295 KC584419 KC584211 KC584130 KC584677 A. petuchovskii M304 KJ443079 KJ443124 KJ443170 KJ443254 KJ649616 – A. photistica CBS 212.86 KC584552 KC584296 KC584420 KC584212 KC584131 KC584678 A. phragmospora CBS 274.70 KC584595 KC584337 KC584462 JN383493 JN383474 KC584721 A. porri CBS 116698 KC584553 KC584297 KC584421 DQ323700 KC584132 KC584679 A. proteae CBS 475.90 KC584597 KC584339 KC584464 AY278842 KC584161 KC584723 A. pseudorostrata CBS 119411 KC584554 KC584298 KC584422 JN383483 AY562406 KC584680 A. radicina CBS 245.67 KC584555 KC584299 KC584423 KC584213 KC584133 KC584681 A. scirpicola CBS 481.90 KC584602 KC584344 KC584469 KC584237 KC584163 KC584728 A. septorioides CBS 106.41 KC584559 KC584303 KC584427 KC584216 KC584136 KC584685 A. septospora CBS 109.38 KC584620 KC584362 KC584487 FJ266489 FJ266500 KC584747 A. shukurtuzii M307 KJ443082 KJ443127 KJ443172 KJ443257 KJ649620 - A. simsimi CBS 115265 KC584560 KC584304 KC584428 JF780937 KC584137 KC584686 A. slovaca A. smyrnii CBS 567.66 CBS 109380 KC584576 KC584561 KC584319 KC584305 KC584444 KC584429 KC584226 AF229456 KC584150 KC584138 KC584702 KC584687 A. solani CBS 116651 KC584562 KC584306 KC584430 KC584217 KC584139 KC584688 A. soliaridae CBS 118387 KC584563 KC584307 KC584431 KC584218 KC584140 KC584689 A. solidaccana CBS 118698 KC584564 KC584308 KC584432 KC584219 KC584141 KC584690 A. sonchi CBS 119675 KC584565 KC584309 KC584433 KC584220 KC584142 KC584691 Alternaria sp. CBS 175.52 KC584577 KC584320 KC584445 KC584227 KC584151 KC584703 A. tagetica CBS 479.81 KC584566 KC584310 KC584434 KC584221 KC584143 KC584692 A. tellustris CBS 538.83 KC584598 KC584340 KC584465 FJ357316 AY562419 KC584724 A. thalictrigena CBS 121712 KC584568 KC584312 KC584436 EU040211 KC584144 KC584694 A. triglochinicola CBS 119676 KC584569 KC584313 KC584437 KC584222 KC584145 KC584695 A. vaccariae CBS 116533 KC584570 KC584314 KC584438 KC584223 KC584146 KC584696 A. vaccariicola CBS 118714 KC584571 KC584315 KC584439 KC584224 KC584147 KC584697 123 Fungal Diversity 123 Fungal Diversity b Fig. 24 Phylogenetic tree generated by maximum parsimony analysis of combined SSU, LSU, ITS, GPDH, tef1 and RPB2 sequence data of Alternaria species. One hundred strains are included in the analyses, which comprised 4056 characters including gaps. The tree was rooted with Stemyphylium herbarium (CBS 191.86) and Pleospora tarda (CBS 714.68). The maximum parsimonious dataset consisted of 3091 constant, 852 parsimony-informative and 113 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 4520 steps (CI = 0.335, RI 0.708, RC = 0.237, HI = 0.665) in the first tree. MP and ML bootstrap values C 50% and Bayesian posterior probabilities C 0.90 are shown respectively near the nodes. Ex-type strains are in bold Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Dothiorella pyrenophora Berk. ex Sacc., Michelia 2 (6): 5 (1880) (1909) Distribution—Worldwide Disease symptoms—Diebacks, cankers, fruit rots. Hosts—Plurivorous on woody hosts. Morphological based identification and diversity Species of this genus were mostly described based on host association, which has led to the introduction of many species names and currently there are 393 epithets in Index Fungorum (2019). Slippers et al. (2013) suggested that host association cannot be considered as an important factor in species delimitation, many names are likely to be synonyms. Phillips et al. (2008) introduced a new genus Spencermartinsia to accommodate dothiorella-like species with apiculate ascospores. However, Yang et al. (2017) based on six-gene phylogeny and a broad taxon sampling considered that Spencermartinsia should be treated as a synonym of Dothiorella. Phillips et al. (2013) listed all cultures available for this genus and provided a phylogenetic tree and a key to the species. In that study 13 species names and 16 unnamed lineages were listed. Hyde et al. (2014), Dissanayake et al. (2016) and Yang et al. (2017) provided updates for the genus. Hyde et al. (2014) accepted 19 species and Dissanayake et al. (2016) accepted 30 species in the genus. After making Spencermartinsia a synonym of Dothiorella Yang et al. (2017) accepted 36 species in this genus. Phillips et al. (2013) differentiated 13 Dothiorella species on the basis of conidiomata and conidial dimensions. However, the dimensions of these characters overlap between species. Therefore, using morphology alone without molecular data is not suitable to define species. Molecular based identification and diversity Recent studies have re-evaluated this genus based on multigene phylogeny of ITS, TUB2 and tef1 sequence data. We reconstruct the phylogeny of Dothiorella based on analyses of a combined ITS and tef1 sequence data (Table 17, Fig. 26). The phylogenetic tree is updated with recently introduced Dothiorella species and corresponds to previous studies (Dissanayake et al. 2016; Yang et al. 2017; Hyde et al. 2018; Phookamsak et al. 2019). In the analyses, it appears that several species are synonyms, such as D. parva/D. guttulata and D. rhamni/D. eriobotryae and possibly others. Therefore, a thorough revision of the genus is recommended to clarify the status of these dubious species. Recommended genetic markers (genus level)—SSU and LSU Recommended genetic markers (species level)—ITS and tef1 Accepted number of species: Currently, 393 species names are listed for Dothiorella in Index Fungorum (2019). Cultures and DNA sequences are available for 46 species, therefore 46 species are currently accepted in Dothiorella. References: Phillips et al. 2013; Dissanayake et al. 2016 (morphology, phylogeny, distribution, hosts), Yang et al. 2017 (morphology and phylogeny) Fusarium Link, Mag. Gesell. naturf. Freunde, Berlin 3(12): 10 (1809) Fusarium is a genus with 20 monophyletic species complexes (Rana et al. 2017). Species formely belonged to F. solani species complex were transferred to genus Neocosmospora based on sexual morph characters and molecular phylogeny (Lombard et al. 2015; Sandoval-Denis and Crous (2018). Fusarium species are saprobes, parasites, endophytes, soil-borne or isolated from water (Rana et al. 2017). Species of Fusarium are economically important fungi as they are responsible for blights, cankers, rots, and wilts of horticultural, ornamental and forest crops in both agricultural and natural ecosystems, worldwide, and also human infections (Rana et al. 2017; Varela et al. 2013; Peraldi et al. 2014; Al-Hatmi et al. 2019; Maryani et al. 2019a, b). In nature, sexual morphs of Fusarium occur less commonly than the asexual morphs (Gräfenhan et al. 2011; Rossman et al. 1999). Classification—Sordariomycetes, Hypocreomycetidae, Hypocreales, Nectriaceae Type species—Fusarium sambucinum Fuckel, Hedwigia 2: 135.1863. Distribution—Worldwide Disease symptoms—blights, cankers, rots, and wilts Plant pathogenic species of this genus have the capability to change their lifestyle to saprotrophic and can survive for long periods as chlamydospores in host tissues. Fusarium species damage their hosts by systemically colonizing and occluding the host xylem (Ploetz et al. 2003). Hosts—Known from many host plant families. 123 Fungal Diversity Fig. 25 Phylogenetic tree generated by maximum likelihood analysis of combined ITS and tef1 sequence data of Diplodia species. Related sequences were obtained from GenBank. Forty nine strains are included in the analyses, which comprise 866 characters including gaps. The tree was rooted with Lasiodiplodia theobromae (CBS 164.96). Tree topology of the ML analysis was similar to the BYPP. The best scoring RAxML tree with a final likelihood value of - 3342.903931 is presented. The matrix had 278 distinct alignment patterns, with 9.02%. % of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.207781, C = 0.297582, G = 0.261770, T = 0.232868; substitution rates AC = 0.993193, AG = 3.566477, AT = 0.787748, CG = 1.607220, CT = 4.471399, GT = 1.000000; gamma distribution shape parameter a = 1.224079. RAxML bootstrap support values C 80% (BT) are shown respectively near the nodes. Bayesian posterior probabilities C 0.5 (PP) indicated as thickened black branches. Ex-type strains are in bold Morphological based identification and diversity species concept of Fusarium much broader (Geiser et al. 2004). It leads to the incorrect and confusing application of species names to toxigenic and pathogenic isolates (Geiser et al. 2004). Species boundaries have been inferred using multi-gene phylogenetic methods, reflecting the species diversity more than morphological treatments (Aoki and O’Donnell 1999; Geiser et al. 2004; O’Donnell 2000; Fusarium was also known from the sexual morphic fungus name Gibberella, which was suppressed in favour of Fusarium by Rossman et al. (2013). Variation and mutation in culture and lack of clear morphological characters for separating species are the main problems which make the 123 Fungal Diversity Table 16 Details of the Diplodia isolates used in the phylogenetic analyses Species Isolate/voucher no ITS tef1 Diplodia africana CBS 120835* EF445343 EF445382 Diplodia africana CBS 121104 EF445344 EF445383 Diplodia agrifolia CBS 132777* JN693507 JQ517317 Diplodia agrifolia UCROK1429 JQ411412 JQ512121 Diplodia alatafructa CBS 124931* FJ888460 FJ888444 Diplodia alatafructa CBS 124933 FJ888478 FJ888446 Diplodia allocellula CBS 130408* JQ239397 JQ239384 Diplodia allocellula CBS 130410 JQ239399 JQ239386 Diplodia arengae MFLU 17-2769 MG762771 MG762774 Diplodia bulgarica CBS 124254* GQ923853 GQ923821 Diplodia bulgarica CBS 124135 GQ923852 GQ923820 Diplodia corticola CBS 112549* AY259100 AY573227 Diplodia corticola CBS 112546 AY259110 DQ458872 Diplodia crataegicola MFLU 15-1311* KT290244 KT290248 Diplodia cupressi Diplodia cupressi CBS 168.87* CBS 261.85 DQ458893 DQ458894 DQ458878 DQ458879 Diplodia estuarina CMW41231* KP860831 KP860676 Diplodia estuarina CMW41230 KP860830 KP860675 Diplodia fraxinii CBS 136010* KF307700 KF318747 Diplodia galiicola MFLU 15-1310* KT290245 KT290249 Diplodia insularis CBS 140350* KX833072 KX833073 Diplodia intermedia CBS 124462* GQ923858 GQ923826 Diplodia intermedia CBS 124134 HM036528 GQ923851 Diplodia malorum CBS 124130* GQ923865 GQ923833 Diplodia malorum CBS 112554 AY259095 DQ458870 Diplodia mutila CBS 112553* AY259093 AY573219 Diplodia mutila CBS 230.30 DQ458886 DQ458869 Diplodia neojuniperi CPC 22753* KM006431 KM006462 EU392279 Diplodia olivarum CBS 121887* EU392302 Diplodia olivarum CBS 121886 EU392297 EU392274 Diplodia pseudoseriata Diplodia pseudoseriata CBS 124906* CBS 124907 EU080927 EU080922 EU863181 EU863179 Diplodia quercivora CBS 133852* JX894205 JX894229 Diplodia rosacearum CBS 141915* KT956270 KU378605 Diplodia rosulata CBS 116470* EU430265 EU430267 Diplodia rosulata CBS 116472 EU430266 EU430268 Diplodia sapinea CBS 393.84* DQ458895 DQ458880 Diplodia sapinea CBS 109725 DQ458896 DQ458881 Diplodia scrobiculata CBS 118110* AY253292 AY624253 Diplodia scrobiculata CBS 109944 DQ458899 DQ458884 Diplodia scrobiculata CBS 113423 DQ458900 DQ458885 Diplodia seriata CBS 112555* AY259094 AY573220 Diplodia seriata CBS 119049 DQ458889 DQ458874 Diplodia subglobosa CBS 124133* GQ923856 GQ923824 Diplodia tsugae CBS 418.64* DQ458888 DQ458873 Ex-type (ex-epitype) strains are in bold and marked with an asterisk* and voucher stains are in bold 123 Fungal Diversity Fig. 26 Phylogenetic tree generated by maximum parsimony analysis of combined ITS and tef1 sequence data of Dothiorella species. Related sequences were obtained from GenBank. Forty eight strains are included in the analyses, which comprised 873 characters including gaps. The tree was rooted with Neofusicoccum parvum (CMW9081) and N. mangiferae (CMW7024). The maximum parsimonious dataset consisted of 572 constant, 204 parsimony- informative and 97 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 891 steps (CI = 0.532, RI 0.738, RC = 0.393, HI = 0.468) in the first tree. MP and ML bootstrap values C 50% and Bayesian posterior probabilities C 0.90 are shown respectively near the nodes. The scale bar indicates 10 changes per site. Ex-type strains are in bold O’Donnell et al. 1998a, b; Ward et al. 2002). A combined phylogenetic analysis of LSU, ITS, RPB2 and new phylogenetic marker acl1 by Gräfenhan et al. (2011), revealed that the early concept of Fusarium is not monophyletic. Fusarium sensu Wollenweber divided into two large groups, basal ‘Fusarium-like clades’, and the other one terminal ‘Fusarium clade’ in the Nectriaceae (Gräfenhan et al. 2011) (Fig. 27). Molecular based identification and diversity 123 ITS and LSU are least informative in species-level identification of Fusarium (O’Donnell et al. 1998a; Hyde et al. 2014). Moreover, non-orthologous copies of the ITS2, which can lead to wrong phylogenetic inferences, can be detected in many species of Fusarium (Geiser et al. 2004; O’Donnell et al. 1998a, b). Generally, for the species-level identification of fungi intron-rich regions of protein-coding Fungal Diversity Table 17 Details of the Dothiorella isolates used in the phylogenetic analyses Species Isolate/voucher no ITS tef1 Dothiorella acacicola CBS 141295 KX228269 KX228376 D. acericola KUMCC 18-0137* MK359449 MK361182 D. alpina CGMCC 3.18001* KX499645 KX499651 D. americana CBS 128309* HQ288218 HQ288262 D. brevicollis CBS 130411* JQ239403 JQ239390 D. californica CBS 141587* KX357188 KX357211 D. capri-amissi CMW 25403* EU101323 EU101368 D. casuarinae CBS 120688* DQ846773 DQ875331 D. citricola ICMP16828* EU673323 EU673290 D. dulcispinae CBS 130413* JQ239400 JQ239387 KT240262 D. eriobotryae CBS 140852* KT240287 D. guttulata MFLUCC 17-0242 KY797637 – D. iberica CBS 115041* AY573202 AY573222 D. iranica IRAN1587C* KC898231 KC898214 D. italica D. juglandis MFLUCC 17-0951 CBS 188.87 MG828897 EU673316 MG829267 EU673283 D. lampangensis MFLUCC 18-0232 MK347758 MK340869 D. longicollis CBS 122068* EU144054 EU144069 D. magnoliae CFCC 51563 KY111247 KY213686 D. mangifericola IRAN1584C* KC898221 KC898204 D. moneti MUCC505* EF591920 EF591971 D. neclivorem DAR80992* KJ573643 KJ573640 D. oblonga CMW 25407* EU101300 EU101345 D. omnivora CBS 140349* KP205497 KP205470 D. parva IRAN1579C* KC898234 KC898217 D. plurivora IRAN1557C* KC898225 KC898208 D. pretoriensis CBS 130404* JQ239405 JQ239392 D. prunicola CBS 124723* EU673313 EU673280 D. rhamni MFLUCC 14-0902* KU246381 – D. rosulata CBS 121760* EU101290 EU101335 D. santali D. sarmentorum MUCC 509* EF591924 EF591975 IMI63581b* AY573212 AY573235 D. sempervirentis IRAN1583C* KC898236 KC898219 D. striata ICMP16824* EU673320 EU673287 D. styphnolobii JZB3150013* MH880849 MK069594 D. symphoricarposicola MFULCC 13-0497* KJ742378 KJ742381 D. tectonae MFLUCC12-0382* KM396899 KM409637 D. thailandica CBS 133991* JX646796 JX646861 D. thripsita BRIP 51876* FJ824738 KJ573639 D. ulmacea CBS 138855* KR611881 KR611910 D. uruguayensis CBS 124908* EU080923 EU863180 D. vidmadera DAR78992* EU768874 EU768881 D. vinea-gemmae DAR81012* KJ573644 KJ573641 D. viticola CBS 117009* AY905554 AY905559 D. westrale DAR80529* HM009376 HM800511 D. yunnana CGMCC 3.17999* KX499643 KX499649 Ex-type (ex-epitype) strains are in bold and marked with an asterisk* and voucher stains are in bold a the tef1 sequence of D. guttulata in GenBank is incorrect, therefore was not included in the analyses 123 Fungal Diversity genes are used as the markers (Geiser et al. 2004). The translation elongation factor 1-a (tef1), which lacks nonorthologous copies of the gene, is highly informative at the species level in Fusarium (Geiser et al. 2004). RPB1 and RPB2 are also very informative gene regions for species identification of Fusarium (O’Donnell et al. 2013; Hyde et al. 2014). Lombard et al. (2018) observed that tef1 and RPB2 genes provide better resolution of the species in the F. oxysporum complex than cmdA and tub2 (Fig. 28, Table 18). Recommended genetic markers (genus level)—ATP citrate lyase (acl1), tef1 and ITS Recommended genetic markers (species level)—calmodulin-encoding gene (cmdA), tub2, tef1, RPB1 and RPB2 Accepted number of species: There are 1552 species epithets in Index Fungorum (2019) under this genus. More than 175 species have DNA sequence data. References: Booth 1971, Rossman et al. 1999 (morphology), Rana et al. 2017, Gräfenhan et al. 2011; Laurence et al. 2014; Lombard et al. 2018, 2019; Maryani et al. 2019a, b; Wang et al. 2019; Nalim et al. 2011 (morphology, phylogeny). Lasiodiplodia Ellis & Everh., Bot. Gaz. 21:92 (1896) According to Clendenin (1896), a fungus causing rot of sweet potatoes imported from Java was identified by Ellis in 1894 as a new genus and he named the fungus Lasiodiplodia tubericola. However, Ellis (1894) did not describe the fungus or publish the new genus. Clendenin (1896) provided a description of the genus and the species, attributing both to Ellis and Everhardt. Griffin and Maublanc (1909) considered that on account of the pycnidial paraphyses, Botryodiplodia theobromae, described by Patouillard and de Lagerheim (1892), was more suitably accommodated in Lasiodiplodia. Since the epithet theobromae (1892) is older than tubericola (1896), L. theobromae should be regarded as the type species of Lasiodiplodia. Neither Patouillard and de Lagerheim (1892) nor Clendenin (1896) referred to any type or other specimens of the genus or species. Pavlic et al. (2004) could not locate the types, and they could not find any specimens from the original hosts or origins. Phillips et al. (2013) designated CBS H-21411 as neotype with CBS 164.96 as culture ex-neotype. The sexual morph has been reported for L. theobromae, but the connection with the asexual morph has not been confirmed (Phillips et al. 2013). Sexual morphs have also been reported for L. pseudotheobromae (Tennakoon et al. 2016), L. gonubiensis (Trakunyingcharoen et al. 2015) and L. lignicola (Phillips et al. 2013) with clear evidence that connects sexual with asexual morphs. 123 Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Lasiodiplodia theobromae (Pat.) Griffon & Maubl., Bull. Soc. mycol. Fr. 25: 57 (1909) Distribution—Worldwide, mostly confined to tropical and sub-tropical regions, but becoming increasingly more common in warm temperate regions. Disease symptoms—Diebacks, cankers, fruit rots. Hosts—Plurivorous on woody hosts Morphological based identification and diversity The pigmented, 1-septate conidia with longitudinal striations together with the pycnidial paraphyses distinguish Lasiodiplodia from all other genera in Botryosphaeriaceae (Phillips et al. 2013). Striations on the conidia distinguish it from Diplodia, the conidiomata paraphyses distinguish it from Neodeightonia, which also has striate conidia. Although Barriopsis has striate conidia and paraphyses, Lasiodiplodia is unique in the Botryosphaeriaceae because striations are visible on immature, hyaline conidia. Although Phillips et al. (2013) differentiated 18 species in Lasiodiplodia on the basis of conidial morphology (especially dimensions) and morphology of the paraphyses, in reality, species in Lasiodiplodia cannot be identified with any confidence from their morphology and molecular data are necessary for definitive identifications. Molecular based identification and diversity Denman et al. (2000) suggested that Lasiodiplodia could be a synonym of Diplodia. When Crous et al. (2006) re-organized Botryosphaeria on the basis of LSU phylogeny they split the genus into 10 genera, but could not resolve the position of Lasiodiplodia or separate it from Diplodia. Following a multi-locus approach (SSU, ITS, LSU, tef1 and TUB2) Phillips et al. (2008) showed that Lasiodiplodia constitutes a clear phylogenetic lineage. For many years, only the type species of Lasiodiplodia (L. theobromae) was mentioned in the phytopathological and mycological literature, and it was regarded as a cosmopolitan, plurivorous pathogen restricted mainly to tropical and sub-tropical regions (Punithalingam 1976, 1980). Soon after the widespread application of DNA-based phylogenies, Pavlic et al. (2004) introduced L. gonubiensis as a new species on the basis of conidial morphology and ITS sequence data. Soon after, Burgess et al. (2006) described three new species (L. crassispora, L. venezuelensis and L. rubropurpurea) from the tropics based on ITS and tef1 sequence data and morphological characters. Alves et al. (2008) also used ITS and tef1 sequence data to reveal two cryptic species in the L. theobromae complex. Over the years more species were introduced and Phillips et al. (2013) listed 18 species and Dissanayake et al. (2016) listed 31 species known from culture. Today Fungal Diversity Fig. 27 Sexual morph of a Fusarium sp. a Herbarium material. b Ascomata on the host. c Section of ascomata. d Section of the ostiolar region. e Peridium in face view. f–h Asci (h in Melzer’s reagent). i, j Ascospores. k Germinating ascospore. l, m Colony on MEA. Scale bars: c = 100 lm, d = 50 lm, e–k = 20 lm the figure stands at 40 (Fig. 29). Apart from L. theobromae, all species have been introduced almost entirely on the basis of DNA sequence phylogenies. Although the phylogenies were derived from analysis of multiple loci (mostly ITS, tef1 and TUB2 and sometimes RPB2) the genealogical concordance phylogenetic species recognition concept (Taylor et al. 2000) has not always been strictly applied and species have been introduced on the basis of minor differences in only one locus. The result is that some species are not well separated phylogenetically (Fig. 29, Table 19), such as L. hyalina and L. thailandica, L. chinensis, L. sterculiae, L. pseudotheobromae, L. pyriformis and L. crassispora. In a detailed study of five loci of 19 Lasiodiplodia species, Cruywagen et al. (2017) concluded that several accepted species (L. viticola, L. missouriana, L. laeliocattleyae, L. brasiliense) may, in fact, be hybrids. There has been no such study of the 16 species introduced after the work of Cruywagen et al. (2017). In view of the questionable status of several species in Lasiodiplodia, there is an urgent need to re-assess all of the species currently accepted in this genus. 123 Fungal Diversity 123 Fungal Diversity b Fig. 28 Phylogram generated from RAxML analysis based on combined RPB1, RPB2 and tef1 sequences of accepted species of Fusarium. Related sequences were obtained from GenBank. One hundred sixty-five taxa are included in the analyses, which comprise 3980 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 in Fusicolla aquaeductuum (NRRL 20696). Tree topology of the ML analysis was similar to the BYPP. The best scoring RAxML tree with a final likelihood value of - 63956.723151 is presented. The matrix had 2254 distinct alignment patterns, with 25.13% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.257298, C = 0.251723, G = 0.248896, T = 0.242083; substitution rates AC = 1.366599, AG = 4.760724, AT = 1.266971, CG = 0.903914, CT = 9.564945, GT = 1.000000; gamma distribution shape parameter a = 1.089091. Maximum likelihood bootstrap support values C70% (BT) and Bayesian posterior probabilities C 0.99 (PP) are given near the nodes respectively Recommended genetic markers (genus level)—SSU and LSU Recommended genetic markers (species level)—ITS, tef1, TUB2 Accepted number of species: Currently, 51 species names are listed for Lasiodiplodia in MycoBank and Index Fungorum (2019). Cultures and DNA sequences are available for 43 species, three of which have been reduced to synonymy under existing names. Thus, 40 species are currently recognised in Lasiodiplodia. References: Phillips et al. 2013 (morphology, phylogeny, distribution, hosts); Dissanayake et al. 2016 (species). Pestalotiopsis Steyaert, Bull. Jard. bot. État Brux. 19: 300 (1949) Pestalotiopsis is an appendage-bearing, 5-celled conidia (asexual coelomycetes) in the family Sporocadaceae (Maharachchikumbura et al. 2014a, b; Jayawardena et al. 2016). The genus was introduced by Steyaert (1949). Pestalotiopsis species are widely distributed throughout 1961; tropical and temperate regions (Guba Maharachchikumbura et al. 2012, 2014a). Pestalotiopsis species have been isolated from dead leaves, bark, twigs, soil, polluted stream water, wood, paper, fabrics, and wool (Guba 1961; Maharachchikumbura et al. 2012, 2014a). Some species have been associated with human and animal infections, and others (e.g. P. guepinii and P. microspora) have also been isolated from extreme environments (Maharachchikumbura et al. 2014b). Classification—Sordariomycetes, Xylariomycetidae, Amphisphaeriales, Sporocadaceae Type species—Pestalotiopsis guepinii (Desm.) Steyaert [as ‘guepini’], Bull. Jard. bot. État Brux. 19(3): 312 (1949) Distribution—Worldwide Disease symptoms—Species of Pestalotiopsis cause a variety of diseases in plants including canker lesions, shoot dieback, leaf spots, needle blight, tip blight, grey blight, scabby canker, severe chlorosis, fruit rots and various postharvest diseases (Maharachchikumbura et al. 2013a, b, 2014a, b). These pathogens reduce production and cause economic loss in apple, blueberry, coconut, chestnut, ginger, grapevine, guava, hazelnut, lychee, mango, orchid, peach, rambutan, tea and wax apple due to diseases (Maharachchikumbura et al. 2013a, b, 2014a, b). Grapevine trunk diseases are the most destructive diseases of grapevines that impact the economic production and longevity of vineyards and even leading to partial or total death of individual plants. Therefore, the initial identification of the causal agent is essential for early control of 2015; these diseases (Jayawardene et al. Maharachchikumbura et al. 2017). Pestalotoid fungi have been reported as pathogens on a variety of grapevine cultivars, causing diseases including grapevine dieback, fruit rot, postharvest disease and severe defoliation and they infect all plant parts including leaves, canes, wood, berries and flowers (Jayawardene et al. 2015; Maharachchikumbura et al. 2017). Pestalotiopsis menezesiana (Bres. & Torr.) Bissett. and P. uvicola (Spegazzini) Bissett, are the most common species recorded from grapevine around the world and especially P. biciliata are associated with trunk 2015; grapevine disease (Jayawardene et al. Maharachchikumbura et al. 2017). Hosts—Broad range of hosts including members of Altingiaceae, Arecaceae, Bromeliaceae, Euphorbiaceae, Myrtaceae, Poaceae, Proteaceae, Rosaceae, Rutaceae, Theaceae and Vitaceae. Morphological based identification and diversity There are around 250 species, most of which were named according to their host associations (Maharachchikumbura et al. 2014a, b). However, Pestalotiopsis species are not hosted specific and are found on a wide range of plants and substrates (Jeewon et al. 2003; Lee et al. 2006; Maharachchikumbura et al. 2014a, b). They exhibit considerable diversity in phenotype, and group together based on similarities in conidial morphology (Jeewon et al. 2003; Maharachchikumbura et al. 2012, 2013a, b, 2014a, b). Considering morphology, conidial length, width, median cell length, the colour of median cells and length of the apical appendages appear to be stable characters within Pestalotiopsis (Jeewon et al. 2003; Maharachchikumbura et al. 2014b). Pestalotiopsis guepinii was considered to be the type species of the genus described from stems and leaves of Camellia japonica collected in France, and is characterised by 5-celled conidia with three concolourous median cells, hyaline terminal cells and simple or unbranched 123 Fungal Diversity Fig. 28 continued appendages arising from the apex of the apical cell (Steyaert 1949; Maharachchikumbura et al. 2014b). Nag Raj (1985) regarded P. maculans as the type species of Pestalotiopsis with P. guepinii as a synonym. Jeewon et al. (2003) also accepted P. maculans clusters with species having concolourous median cells based on phylogenetic analysis of ITS sequence data and that P. karstenii might be a synonym of P. maculans (Maharachchikumbura et al. 2014b). Most Pestalotiopsis species lack sexual morphs. The sexual morph of Pestalotiopsis was treated as Pestalosphaeria Barr, with the type species Pestalosphaeria concentrica collected from grey-brown spots on living leaves 123 of Rhododendron maximum in North Carolina, USA (Maharachchikumbura et al. 2014b). Pestalosphaeria concentrica is characterised by immersed, subglobose ascomata and unitunicate, cylindrical asci with a J ? apical ring; ascospores uniseriate in the ascus, ellipsoid, pale dull brown and 2-septate (Maharachchikumbura et al. 2014b). Pestalotiopsis species have the ability to switch lifemodes as endophytes, pathogens and saprobes (Hu et al. 2007; Maharachchikumbura et al. 2012). Therefore, many endophytic and plant pathogenic Pestalotiopsis species persist as saprobes and have been isolated from dead leaves, bark and twigs (Maharachchikumbura et al. 2012, 2013a, b, 2014b). Fungal Diversity Table 18 Details of the Fusarium isolates used in the phylogenetic analyses Species Isolate/voucher no RPB1 RPB2 tef1 Fusarium anguioides NRRL 25385*; ATCC 66485 JX171511 JX171624 MH742689 F. acaciae-mearnsii NRRL 26755 KM361640 KM361658 AF212449 F. acuminatum NRRL 36147; CBS 109232 HM347174 GQ505484 GQ505420 F. agapanthi NRRL 54463* KU900620 KU900625 KU900630 F. albidum NRRL 22152 JX171492 JX171605 – F. albosuccineum NRRL 20459 JX171471 JX171585 – F. algeriense NRRL 66647*; CBS 142638; IL-79 MF120488 MF120499 – F. ananatum CBS 118516* LT996188 LT996137 KU604416 F. andiyazi NRRL 31727; CBS 119857 LT996189 LT996138 KP662901 F. anthophilum NRRL 13602; CBS 737.97 LT996190 LT996139 KU711685 F. arcuatisporum F. armeniacum CGMCC3.19493*; LC12147 NRRL 6227 MK289799 JX171446 MK289739 JX171560 MK289584 HM744692 F. asiaticum NRRL 13818*; CBS 110257 JX171459 JX171573 AF212451 F. avenaceum NRRL 54939 JX171551 JX171663 MH582391 F. aywerte NRRL 25410 JX171513 JX171626 KU171717 F. babinda NRRL 25539; CBS 396.96 JX171519 JX171632 MH742712 F. begoniae CBS 403.97*; NRRL 25300 LT996191 LT996140 AF160293 F. beomiforme NRRL 25174; CBS 740.97 – JX171619 – F. brachygibbosum NRRL 13829 JX171460 JX171574 – F. buharicum NRRL 13371; CBS 796.70 JX171449 JX171563 – F. bulbicola NRRL 13618*; CBS 220.76 KF466394 KF466404 KF466415 F. burgessii CBS 125537*; RBG 5319 KJ716217 HQ646393 HQ667149 F. callistephi CBS 187.53* – MH484905 MH484966 F. carminascens CBS 144738*; CPC 25800 – MH484937 MH485028 F. celtidicola MFLUCC 16-0751* – MH576580 – F. citri CGMCC3.19467*; LC6896 MK289828 MK289771 MK289617 F. citricola F. coicis CBS 142421*; CPC 27805 NRRL 66233*; RBG5368 LT746290 KP083269 LT746310 KP083274 LT746197 KP083251 F. commune NRRL 28387 – JX171638 KU171720 F. concentricum NRRL 25181*; CBS 450.97 LT996192 JF741086 AF160282 F. concolor NRRL 13459*; CBS 961.87 JX171455 JX171569 MH742681 F. contaminatum CBS 114899* – MH484901 MH484992 F. continuum F201128 KM520389 KM236780 KM236720 F. convolutans CBS 144207*; CPC 33733 LT996193 LT996141 LT996094 F. cugenangense InaCCF984* LS479560 LS479308 – F. culmorum NRRL 25475; CBS 417.86 JX171515 JX171628 KY873384 F. cuneirostrum NRRL 31104 – EU329558 EF408413 F. curvatum CBS 238.94; NRRL 26422; PD 94/184 – MH484893 MH484984 F. cyanostomum NRRL 53998 JX171546 JX171658 – F. dactylidis NRRL 29298* KM361654 KM361672 DQ459748 F. denticulatum NRRL 25302; CBS 735.97 LT996195 LT996143 AF160269 F. desaboruense F. dlaminii InaCC F950 NRRL 13164*; CBS 119860 LS479870 KU171681 LS479852 KU171701 – MK639039 F. duoseptatum InaCC F916* LS479495 LS479239 – F. elaeidis CBS 217.49*; NRRL 36358 – MH484870 MH484961 F. enterolobii CPC 27190 – LT746312 LT746199 F. equiseti NRRL 13405 – GQ915491 GQ915507 F. fabacearum CBS 144743*; CPC 25802 – MH484939 MH485030 123 Fungal Diversity Table 18 (continued) Species Isolate/voucher no RPB1 RPB2 tef1 F. ficicrescens CBS 125178* – KT154002 KP662899 F. flocciferum NRRL 25473 JX171514 JX171627 – F. foetens NRRL 38302 JX171540 JX171652 GU170559 F. fracticaudum CMW 252374 LT996196 LT996144 KJ541059 F. fractiflexum NRRL 28852* – LT575064 AF160288 F. fredkrugeri CBS 144209*; CPC 33747 LT996199 LT996147 LT996097 F. fujikuroi NRRL 13566 JX171456 JX171570 – F. gaditjirrii F. gamsi NRRL 45417 CBS 143610*; CPC 30862; OrSaAg4 – – JX171654 LT970760 KU171724 LT970788 F. globosum NRRL 26131*; CBS 428.97 KF466396 KF466406 KF466417 F. glycines CBS 144746*; CPC 25808 – MH484942 MH485033 F. gossypinum CBS 116613* – MH484909 MH485000 F. graminearum NRRL 31084; CBS 123657 JX171531 JX171644 HM744693 F. grosmichelii InaCC F833* LS479548 LS479295 LS479744 F. guilinense CGMCC3.19495*; LC12160 MK289831 MK289747 MK289594 F. guttiforme NRRL 22945 JX171505 JX171618 – F. hainanense CGMCC3.19478*; LC11638 MK289833 MK289735 MK289581 F. heterosporum NRRL 20693; CBS 720.79 JX171480 JX171594 – F. hexaseptatum InaCC F866* – LS479359 LS479805 F. hoodiae CBS 132474* – MH484929 MH485020 F. hostae NRRL 29889 JX171527 JX171640 AY329034 F. inflexum NRRL 20433 – JX171583 AF008479 F. ipomoeae F. iranicum CGMCC3.19496*; LC12165 CBS 143608*; CPC 30860; OrSaAg2 MK289859 – MK289752 LT970757 MK289599 LT970785 F. irregulare CGMCC3.19489*; LC7188 MK289863 MK289783 MK289629 F. kalimantanense InaCC F917* LS479497 LS479241 LS479690 F. konzum CBS 119849* LT996200 LT996148 LT996098 F. kotabaruense InaCC F963* LS479875 LS479859 LS479445 F. kuroshium CBS 142642*; UCR3641 KX262236 KX262256 KX262216 F. kyushuense NRRL 25349 – GQ915492 GQ915508 F. lacertarum NRRL 20423; CBS 130185 HM347137 JX171581 GQ505593 F. lactis NRRL 25200*; CBS 411.97 LT996201 LT996149 AF160272 F. langsethiae NRRL 54940 JX171550 JX171662 – F. languescens CBS 645.78*; NRRL 36531 – MH484880 MH484971 F. lateritium NRRL 13622 JX171457 JX171571 AY707173 F. libertatis CBS 144749*; CPC 28465 – MH484944 MH485035 F. longipes NRRL 13368 JX171448 JX171562 – F. luffae CGMCC3.19497*; LC12167 MK289869 MK289754 MK289601 F. lumajangense F. lyarnte InaCC F872* NRRL 54252; CBS 125536 – JX171549 LS479850 JX171661 LS479441 – F. mangiferae NRRL 25226*; BBA 69662 JX171509 JX171622 – F. miscanthi NRRL 26231 – JX171634 KU171725 F. mundagurra NRR L66235*; RBG5717 KP083272 KP083276 MK639058 F. nanum CGMCC3.19498*; LC12168 MK289871 MK289755 MK289602 F. napiforme CBS 748.97*; NRRL 13604 HM347136 EF470117 KU604409 GQ505402 F. nelsonii NRRL 13338 JX171447 JX171561 F. newnesense NRRL 66237; RBG5443 KP083271 KP083277 KJ397074 F. nirenbergiae CBS 840.88* – MH484887 MH484978 123 Fungal Diversity Table 18 (continued) Species Isolate/voucher no RPB1 RPB2 tef1 F. nisikadoi NRRL 25179; CBS 742.97 JX171507 JX171620 – F. nurragi NRRL 36452; CBS 392.96 JX171538 JX171650 – F. nygamai NRRL 13448*; CBS 749.97 LT996202 EF470114 AF160273 F. odoratissimum InaCC F822* LS479618 LS479386 – F. oligoseptatum NRRL 62579*; FRC S- 2581; MAFF 246283; CBS 143241 KC691596 KC691656 KC691538 F. oxysporum CBS 144134* – MH484953 MH485044 F. palustre NRRL 54056* KT597718 KT597731 – F. paranaense F. parvisorum CML1830* CBS 137236*; FCC 5407; CMW 25267 – – KF680011 LT996150 KF597797 KJ541060 F. pernambucanum MUM 1862*; URM 7559 MH668869 – – F. petersiae CBS 143231* MG386139 MG386150 MG386159 F. pharetrum CBS 144751*; CPC 30824 – MH484952 MH485042 F. phialophorum InaCC F971* LS479545 LS479292 LS479741 F. phyllophilum NRRL 13617*; CBS 216.76 KF466399 KF466410 KF466421 F. pisi NRRL 22278 – EU329501 AF178337 F. poae NRRL 13714 JX171458 JX171572 – F. praegraminearum NRRL 39664* KX260125 KX260126 KX260120 F. proliferatum NRRL 22944; CBS 217.76 JX171504 JX171617 – F. pseudensiforme NRRL 46517 KC691615 KC691645 KC691555 F. pseudocircinatum NRRL 22946*; CBS 449.97 LT996204 LT996151 AF160271 F. pseudograminearum NRRL 28062*; CBS 109956 JX171524 JX171637 AF212468 F. pseudonygamai NRRL 13592*; CBS 417.97 LT996205 LT996152 AF160263 F. purpurascens F. ramigenum InaCC F886* NRRL 25208*; CBS 418.98 – KF466401 LS479385 KF466412 LS479827 KF466423 F. redolens NRRL 22901; CBS 743.97 – KU171708 KU171728 F. riograndense HCF3* – KX534003 KX534002 F. roseum NRRL 22187 JX171493 JX171606 – F. sacchari NRRL 13999; CBS 223.76 JX171466 JX171580 KU711669 F. salinense CBS 142420*; CPC 26973 LT746286 LT746306 LT746193 F. sangayamense InaCC F960* LS479537 LS479283 – F. sarcochroum NRRL 20472; CBS 745.79 JX171472 JX171586 – F. scirpi NRRL 13402 JX171452 JX171566 GQ505592 F. sibiricum NRRL 53430* – HQ154472 HM744684 F. siculi CBS 142422*; CPC 27188 LT746299 LT746327 LT746214 F. sororula CBS 137242* LT996206 LT996153 – F. sporotrichioides NRRL 3299 JX171444 JX171558 HM744665 F. staphyleae NRRL 22316 JX171496 JX171609 MH582426 F. stercicola CBS 142481*; DSM 106211 – KY556552 KY556524 F. stilboides F. subglutinans NRRL 20429; ATCC 15662 NRRL 22016*; CBS 747.97 JX171468 JX171486 JX171582 JX171599 – HM057336 F. sublunatum NRRL 13384*; CBS 189.34 JX171451 JX171565 – F. subtropicale NRRL 66764*; CBS 144706 MH706972 MH706973 MH706974 F. succisae NRRL 13613; CBS 219.76 LT996207 LT996154 AF160289 F. sudanense CBS 454.97*; NRRL 25451 LT996208 LT996155 KU711697 F. sulawesiense InaCC F940* – LS479855 LS479443 F. tanahbumbuense InaCC F965* LS479877 LS479863 LS479448 F. tardichlamydosporum InaCC F958* – LS479280 LS479729 F. tardicrescens NRRL 36113* LS479474 LS479217 LS479665 123 Fungal Diversity Table 18 (continued) Species Isolate/voucher no RPB1 RPB2 tef1 F. terricola CBS 483.94* LT996209 LT996156 KU711698 F. thapsinum NRRL 22045; CBS 733.97 JX171487 JX171600 AF160270 F. tjaetaba NRRL66243*; RBG5361 KP083267 KP083275 KP083263 F. tjaynera NRRL66246*; RBG5367 KP083268 KP083279 – F. torreyae NRRL 54149 JX171548 HM068359 HM068337 F. torulosum NRRL 22748; NRRL 13919 JX171502 JX171615 – F. transvaalense CBS 144211*; CPC 30923 LT996210 LT996157 LT996099 F. tricinctum F. triseptatum NRRL 25481*; CBS 393.93 CBS 258.50*; NRRL 36389 JX171516 – HM068327 MH484873 MH582379 MH484964 F. udum NRRL 22949; CBS 178.32 LT996220 LT996172 AF160275 F. venenatum CBS 458.93* – KM232382 KM231942 F. verrucosum NRRL 22566, BBA 64786 – JX171613 – F. verticillioides NRRL 20956 JX171485 JX171598 – F. veterinarium CBS 109898*; NRRL 36153 – MH484899 MH484990 F. volatile CBS 143874* – LR596006 LR596007 F. witzenhausenense CBS 142480* – KY556553 KY556525 F. xylarioides NRRL 25486; CBS 258.52 JX171517 JX171630 AY707136 F. caatingaense MUM 1859*; URM 6779 MH668845 LS398495 LS398466 F. goolgardi NRRL 66250*; RBG5411 KP083270 KP083280 KP101123 F. humuli CGMCC3.19374*; CQ1039 MK289840 MK289724 MK289570 Fusicolla aquaeductuum NRRL 20686* JX171476 JX171590 – Ex-type (ex-epitype) strains are in bold and marked with an asterisk* and voucher stains are in bold Pestalotiopsis species that were isolated as endophytes are important in the discovery of novel compounds with medicinal, agricultural and industrial applications (Maharachchikumbura et al. 2014b; Xu et al. 2010, 2014). Pestalotiopsis species are a rich source for bioprospecting compared to other fungal genera, and more than 100 compounds have been isolated from Pestalotiopsis (Maharachchikumbura et al. 2014b; Xu et al. 2010, 2014). Molecular based identification and diversity Maharachchikumbura et al. (2012) tested with 10 gene regions to resolve species boundaries in Pestalotiopsis (actin, calmodulin, glutamine synthase, glyceraldehyde-3phosphate dehydrogenase, ITS, LSU, 18S nrDNA, RNA polymerase II, tef1 and TUB2). Maharachchikumbura et al. (2014b) used phylogenetic analysis of combined ITS, TUB2 and tef1 genes to successfully resolve Pestalotiopsis species (Fig. 30, Table 20). Recommended genetic marker (genus level)—LSU (as outlined in Maharachchikumbura et al. 2012) Recommended genetic markers (species level)—ITS, TUB2 and tef1 (as outlined in Maharachchikumbura et al. 2012) 123 Accepted number of species: There are 360 epithets in Index Fungorum in this genus, however, 75 species with DNA sequence data are accepted. References: Maharachchikumbura et al. 2013a, b, 2014b, 2016 (morphology, phylogeny) Stagonosporopsis Died. emend. Aveskamp et al., Stud. Mycol. 65: 44. 2010 Stagonosporopsis is a coelomycetous genus in the family Didymellaceae (de Gruyter et al. 2013), accommodating several important phytopathogenic species. Some of the species have described sexual forms in Didymella (Diedicke 1912; Aveskamp et al. 2010). Some Stagonosporopsis species have quarantine importance. Stagonosporopsis andigena is listed in Annex IAI by European Union (EU), meaning its introduction to EU is prohibited. This pathogen is also listed in the A1 list by the European and Mediterranean Plant Protection Organization (EPPO 2019). Stagonosporopsis chrysanthemi is another species listed in A2 list by EPPO (EPPO 2019). Classification—Dothideomycetes, Pleosporomycetidae, Pleosporales, Didymellaceae Type species—Stagonosporopsis boltshauseri (Sacc.) Died. 1912 Distribution—Worldwide Fungal Diversity Fig. 29 Phylogenetic tree generated by maximum likelihood analysis of combined ITS and tef1 sequence data of Lasiodiplodia species. Related sequences were obtained from GenBank. Forty nine strains are included in the analyses, which comprise 866 characters including gaps. The tree was rooted with Barriopsis tectonae and B. iraniana. Tree topology of the ML analysis was similar to MP and BYPP. The best scoring RAxML tree with a final likelihood value of - 3733.342990 is presented. The matrix had 253 distinct alignment patterns, with 4.41% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.211797, C = 0.285190, G = 0.260783, T = 0.242230; substitution rates AC = 0.983905, AG = 3.303939, AT = 1.281593, CG = 0.950258, CT = 5.553417, GT = 1.000000; gamma distribution shape parameter a = 0.221126. RAxML bootstrap support values C 80% are shown respectively near the nodes. Bayesian posterior probabilities C 0.5 (BYPP) indicated as thickened black branches. Ex-type strains are in bold Disease symptoms—the Black blight of potato, gummy stem blight, ray blight All plant parts may be attacked by S. chrysanthemi and S. inoxydabilis, however, flowers and cuttings are highly susceptible. Death of flowers and buds, a necrotic lesion on leaves and peduncles of unopened buds, soft rot of cortex of roots and discolouration of bark are the main symptom of the disease. Eventually, plant death occurs (Fox 1998; Pethybridge et al. 2008). In gummy stem blight of cucurbits, symptoms can be observed on all above ground and reproductive parts. Leaf spots are the main diagnostic character of this disease. Most of the circular or triangular shaped spots start at the margin of the leaf or extend towards the margin. The centre of the leaf spot is a lighter shade of brown than the surrounding portion. As leaf spots coalesce leaf blights occur. Actively expanding lesions on leaves, petioles, and pedicels often appear as water-soaked. Cankers may form on crowns, main stems and vines (Keinath 2013). Stagonosporopsis andigena the black blight of potato causal agent affects leaves, petioles and stems causing lesions and premature leaf drop, but does not infect the underground parts. On leaves, the pathogen causes small, blackish concentric lesions. The initial symptoms can be observed on the lower leaves, however, as the disease progresses lesions may also develop in upper leaves as well. Lesions may coalesce and severely affected leaves may turn blackish giving a scorched appearance (EFSA panel on plant health 2019). Hosts—Amaranthaceae, Asteraceae, Campanulaceae, Caryophyllaceae, Cucurbitaceae, Fabaceae, Lamiaceae, Pinaceae, Ranunculaceae, Solanaceae and Valerianaceae. 123 Fungal Diversity Table 19 Details of the Lasiodiplodia isolates used in the phylogenetic analyses Species Isolate/voucher no ITS tef1 Lasiodiplodia avicenniae CBS 139670* KP860835 KP860680 L. avicenniarum MFLUCC 17-2591* MK347777 MK340867 L. brasiliense CMM 4015* JX464063 JX464049 L. bruguierae CBS 139669* KP860832 KP860677 L. caatinguensis CMM 1325* KT154760 KT008006 L. chinensis CGMCC 3.18061* KX499889 KX499927 L. chonburiensis MFLUCC 16-0376* MH275066 MH412773 L. cinnamomi CFCC 51997* MG866028 MH236799 L. citricola CBS 124707* GU945354 GU945340 L. crassispora CBS 118741* DQ103550 EU673303 L. euphorbiicola CMM 3609* KF234543 KF226689 L. exigua CBS 137785* KJ638317 KJ638336 L. gilanensis CBS 124704* GU945351 GU945342 L. gonubiensis CBS 115812* AY639595 DQ103566 L. gravistriata L. hormozganensis CMM 4564* CBS 124709* KT250949 GU945355 KT250950 GU945343 L. hyalina CGMCC 3.17975* KX499879 KX499917 L. iraniensis CBS 124710* GU945346 GU945334 L. laeliocattleyae CBS 167.28* KU507487 KU507454 L. lignicola CBS 134112* JX646797 KU887003 L. macrospora CMM 3833* KF234557 KF226718 L. mahajangana CBS 124925* FJ900595 FJ900641 L. margaritacea CBS 122519* EU144050 EU144065 L. mediterranea CBS 137783* KJ638312 KJ638331 L. missouriana CBS 128311* HQ288225 HQ288267 L. pandanicola MFLUCC 16-0265* MH275068 MH412774 L. parva CBS 456.78* EF622083 EF622063 L. plurivora CBS 120832* EF445362 EF445395 L. pontae CMM 1277* KT151794 KT151791 L. pseudotheobromae CBS 116459* EF622077 EF622057 L. pyriformis L. rubropurpurea CBS 121770* EU101307 EU101352 CBS 118740* DQ103553 EU673304 L. sterculiae CBS 342.78* KX464140 KX464634 L. subglobosa CMM 3872* KF234558 KF226721 L. swieteniae MFLUCC 18-0244* MK347789 MK340870 L. thailandica CBS 138760* KJ193637 KJ193681 L. theobromae CBS 164.96* AY640255 AY640258 L. venezuelensis CBS 118739* DQ103547 EU673305 L. viticola CBS 128313* HQ288227 HQ288269 L. vitis CBS 124060* KX464148 KX464642 Ex-type (ex-epitype) strains are in bold and marked with an asterisk* and voucher stains are in bold Morphological based identification and diversity Stagonosporopsis is characterized by ellipsoidal to subglobose, aseptate to 3 septate conidia and sexual morph with ellipsoidal, fusiform or obovoid, 1 septate ascospore (Aveskamp et al. 2010; Chen et al. 2015). Stagonosporopsis was originally separated from Ascochyta 123 by Diedicke (1912) based on the occasional formation of multi-septate (Stagonospora-like) conidia. In the phylogenetic reassessment of Didymellaceae (Aveskamp et al. 2010) based on the sequences LSU and ITS of the nrDNA and TUB2 region, multiple Phoma species, including P. ligulicola, were recovered in a high supported clade with the interpretive types of the genus Stagonosporopsis; S. Fungal Diversity Fig. 30 Phylogram generated from RAxML analysis based on combined ITS, TUB2 and tef1 sequences of all the accepted species of Pestalotiopsis. Related sequences were obtained from GenBank. Seventy-nine taxa are included in the analyses, which comprise 1581 characters including gaps. The tree was rooted in Neopestalotiopsis cubana (CBS 600.96) and N. saprophytica (MFLUCC 12-0282). Tree topology of the ML analysis was similar to the BYPP and MP. The best scoring RAxML tree with a final likelihood value of - 12269.881063 is presented. The matrix had 763 distinct alignment patterns, with 15.79% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.234129, C = 0.293516, G = 0.211518, T = 0.260837; substitution rates AC = 1.189917, AG = 3.402399, AT = 1.153875, CG = 1.001451, CT = 4.301074, GT = 1.000000; gamma distribution shape parameter a = 0.283001. The maximum parsimonious dataset consisted of 948 constant, 450 parsimony-informative and 183 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 1962 steps (CI = 0.498, RI = 0.697, RC = 0.347, HI = 0.502) in the first tree. RAxML and maximum parsimony bootstrap support value C 50% and BYPP C 0.90 values are shown near the nodes. The scale bar indicates 10 changes per site. The ex-type strains are in bold actaeae (Boerema 1997, Boerema et al. 2004). In addition, S. tanaceti shows morphological similarity to S. inoxydabilis but can be differentiated by the faster growth rate, larger conidia, presence of chlamydospores, and lack of ascomata in culture (Vaghefi et al. 2012). Morphological characters overlap between the species in this genus and species are primarily separated based on molecular data. Molecular based identification and diversity Most comprehensive multigene phylogeny analyses for this genus were performed by Aveskamp et al. (2010), Vaghefi 123 Fungal Diversity Table 20 Details of Pestalotiopsis the isolates used in the phylogenetic analyses 123 Species Isolate/voucher no ITS TUB2 tef1 Pestalotiopsis adusta ICMP 6088* JX399006 JX399037 JX399070 P. aggestorum LC6301* KX895015 KX895348 KX895234 P. anacardiacearum IFRDCC 2397* NR120255.1 KC247155 KC247156 P. arceuthobii CBS 434.65* NR147561 KM199427 KM199516 P. arengae CBS 331.92* NR147560 KM199426 KM199515 P. australasiae CBS 114126* NR147546 KM199409 KM199499 P. australis CBS 114193* KM199332 KM199383 KM199475 P. biciliata CBS 124463* KM199308 KM199399 KM199505 P. brachiata LC2988* KX894933 KX895265 KX895150 P. brassicae CBS170.26* NR147562 – KM199558 P. camelliae MFLUCC12-0277* NR120188 JX399041 JX399074 P. chamaeropis CBS 186.71* KM199326 KM199391 KM199473 P. clavata MFLUCC12-0268* JX398990 JX399025 JX399056 P. colombiensis CBS 118553* NR147551 KM199421 KM199488 P. digitalis P. dilucida ICMP 5434* LC3232* KP781879 KX894961 KP781883 KX895293 – KX895178 P. diploclisiae CBS 115587* NR147552 KM199419 KM199486 P. diversiseta MFLUCC12-0287* NR120187 JX399040 JX399073 P. dracontomelon MFUCC 10-0149* KP781877 – KP781880 P. ericacearum IFRDCC 2439* KC537807 KC537821 KC537814 P. formosana NTUCC 17-009* MH809381 MH809385 MH809389 P. furcata MFLUCC12-0054* JQ683724 JQ683708 JQ683740 P. gaultheria IFRD 411-014* KC537805 KC537819 KC537812 P. gibbosa NOF3175* LC311589 LC311590 LC311591 P. grevilleae CBS 114127* NR147548 KM199407 KM199504 P. hawaiiensis CBS 114491* NR147559 KM199428 KM199514 P. hollandica CBS 265.33* KM199328 KM199388 KM199481 P. humus CBS 336.97* KM199317 KM199420 KM199484 P. inflexa MFLUCC12-0270* JX399008 JX399039 JX399072 P. intermedia MFLUCC12-0259* JX398993 JX399028 JX399059 P. italiana P. jester MFLUCC12-0657* KP781878 KP781882 KP781881 CBS 109350* KM199380 KM199468 KM199554 P. jiangxiensis LC4399* KX895009 KX895341 KX895227 P. jinchanghensis LC6636* KX895028 KX895361 KX895247 P. kenyana CBS 442.67* KM199302 KM199395 KM199502 P. knightiae CBS 114138* KM199310 KM199408 KM199497 P. licualacola HGUP 4057* KC492509 KC481683 KC481684 P. linearis MFLUCC12-0271* JX398992 JX399027 JX399058 P. longiappendiculata LC3013* KX894939 KX895271 KX895156 KX895223 P. lushanensis LC4344* KX895005 KX895337 P. macadamiae BRIP 63738b* KX186588 KX186680 KX186621 P. malayana CBS 102220* NR147550 KM199411 KM199482 P. monochaeta CBS 144.97* KM199327 KM199386 KM199479 P. montellica MFLUCC12-0279* JX399012 JX399043 JX399076 P. neolitseae NTUCC 17-011* MH809383 MH809387 MH809391 P. novae-hollandiae P. olivaceae CBS 130973* PSHI2002* NR147557 AY687883 KM199425 DQ333580 KM199511 – P. oryzae CBS 353.69* KM199299 KM199398 KM199496 P. pallidotheae MAFF 240993* NR111022 LC311584 LC311585 P. papuana CBS 887.96* KM199318 KM199415 KM199492 Fungal Diversity Table 20 (continued) Species Isolate/voucher no ITS TUB2 tef1 P. parva CBS 265.37* KM199312 KM199404 KM199508 P. photinicola GZCC 16-0028* KY092404 KY047663 KY047662 P. portugalica CBS 393.48* KM199335 KM199422 KM199510 P. rhizophorae MFLUCC17-0416* MK764283 MK764349 MK764327 P. rhododendri IFRDCC 2399* NR120265 KC537818 KC537811 P. rhodomyrtus HGUP 4230* KF412648 KF412642 KF412645 P. rosea MFLUCC12-0258* JX399005 JX399036 JX399069 P. scoparia CBS 176.25* KM199330 KM199393 KM199478 P. shorea MFLUCC12-0314* KJ503811 KJ503814 KJ503817 P. spathulata CBS 356.86* NR147558 KM199423 KM199513 P. telopeae CBS 114161* NR147545 KM199403 KM199500 P. thailandica MFLUCC17-1616* MK764285 MK764351 MK764329 P. trachicarpicola IFRDCC 2440* NR120109 JQ845945 JQ845946 P. unicolor MFLUCC12-0276* JX398999 JX399030 – P. verruculosa P. yanglingensis MFLUCC12-0274* LC4553* NR120185 KX895012 – KX895345 JX399061 KX895231 P. yunnanensis HMAS 96359* AY373375 – – Ex-type (ex-epitype) strains are in bold and marked with an asterisk* and voucher stains are in bold et al. (2012), Hyde et al. (2014), Chen et al. (2015, 2017) and Jayasiri et al. (2019). Five-marker phylogeny of the Stagonosporopsis spp. for which these DNA sequence data are available is shown (Table 21). Identification of Stagonosporopsis species associated with ray blight of Asteraceae can be achieved through multi-locus sequence typing (Aveskamp et al. 2010; Vaghefi et al. 2012) and also with a species-specific multiplex PCR assay developed by Vaghefi et al. (2016). This assay is based on a four-primer PCR that targets the intergenic spacer of the nrDNA of the ray blight pathogens, producing species-specific amplicons of * 560 in S. chrysanthemi, * 630 bp in S. inoxydabilis and * 400 bp in S. tanaceti, which can be easily differentiated on an agarose gel (Vaghefi et al. 2016). This study reconstructs the phylogeny of Stagonosporopsis based on analyses of a combined ITS, LSU, RPB2 and TUB2 sequence data (Fig. 31). The phylogenetic tree is updated with recently introduced Stagonosporopsis species and corresponds to previous studies (Chen et al. 2017, Jayasiri et al. 2019). Recommended genetic marker (genus level)—ITS Recommended genetic markers (species level)—TUB2 and RPB2 Accepted number of species: There are 55 species in Index Fungorum (2019) and only 24 species are accepted/ have molecular data in this genus. References: Chen et al. 2015, 2017, Jayasiri et al. 2019 (morphology, phylogeny). Verticillium Nees, Syst. Pilze (Würzburg): 57 (1816) [1816-17] The genus Verticillium Nees was introduced by Nees von Esenbeck (1816) for a single saprotrophic species, V. tenerum Nees, which was proposed as the type species. Zare et al. (2004) synonymized V. tenerum under Acrostalagmus luteoalbus (Link) Zare, W. Gams & Schroers, and Gams et al. (2005) proposed V. dahliae Kleb. as the conserved type of the genus Verticillium. Verticillium includes several plant pathogenic species that infect trees, insects, mushrooms and, in particular, dicotyledonous plants: V. dahliae Kleb., V. albo-atrum Reinke et Berth., V. nigrescens Pethybr., V. nubilum Pethybr., V. tricorpus Isaac., V. theobromae (Turc.) Mas. & Hughes and V. fungicola (Preuss) Hassebrauk (Pegg and Brady 2002). Zare et al. (2007) assigned V. nigrescens to the genus Gibellulopsis and V. theobromae to Musicillium. Zare and Gams (2008) assigned V. fungicola to the genus Lecanillium. Verticillium dahliae and V. albo-atrum are the two most notorious species which cause Verticillium wilt diseases in a wide range of mainly dicotyledonous hosts and result in billions of dollars of damage annually in crop losses worldwide (Pegg and Brady 2002; Barbara and Clewes 2003; Inderbitzin et al. 2011). Verticillium species, in particular, V. dahliae and V. alboatrum, can infect a wide range of plant species. Many hosts of Verticillium species were given by different mycologists, e.g., Van der Meer (1925); Rudolph (1931); Engelhard and Carter (1956); Parker (1959); Stark (1961); Devaux and Sackston (1966); Himelick (1969), including 123 Fungal Diversity growth and premature defoliation. Olive- green to black streaks can be observed in the sapwood of infected branches. In cross sections, vascular tissue appears as a dark ring or pinpoint dark spots. Initial symptoms can occur on one side of the tree or the entire plant (Fradin and Thomma 2006; Blum et al. 2018). Hosts—Species of this genus have a broad host range including members of Amaranthaceae, Amaryllidaceae, Asteraceae, Brassicaceae, Musaceae, Pinaceae, Rosaceae, Rubiaceae, Sapindaceae, Solanaceae, Theaceae, Vitaceae and Zingiberaceae (Farr and Rossman 2019). high-value crop plants, e.g., cotton (Land et al. 2016), lettuce (Garibaldi et al. 2007; Powell et al. 2013), mango (Baeza-Montanez et al. 2010; Ahmed et al. 2014), gold kiwifruit (Auger et al. 2009), bean (Berbegal and Armengol 2009; Sun et al. 2016; Blomquist et al. 2017), watermelon (Bruton et al. 2007), olive tree (Lo Giudice et al. 2010; Kaliterna et al. 2016), potato (Pace-Lupi et al. 2006), pumpkin (Rampersad 2008). The most comprehensive hosts’ list was provided by Pegg and Brady (2002). Classification—Sordariomycetes, Hypocreomycetidae, Glomerellales, Plectosphaerellaceae Type species—Verticillium dahliae Kleb., Mykol. Zentbl. 3: 66 (1913) Distribution—Worldwide Disease symptoms—Wilt Wilt caused by Verticillium species is a serious fungal disease that causes injury or death to many plant species. Symptoms of this disease vary according to the host species and to environmental conditions including sudden wilting of small branches, yellowing of foliage, stunt There are 270 records in Index Fungorum (2019) and 288 records in MycoBank (Crous et al. 2004) in this genus. Most of the species have been transferred to other genera, e.g., Gibellulopsis (Zare et al. 2007), Haptocillium (Zare and Gams 2001b), Lecanicillium (Zare and Gams 2001a), Musicillium (Zare et al. 2007), Pochonia (Zare and Gams 2001a, b), Simplicillium (Zare and Gams 2001a). Only ten Fig. 31 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, LSU, RPB2 and TUB2 sequence data of Stagonosporopsis species. Related sequences were obtained from GenBank. Thirty-two are included in the analyses, which comprise 2756 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 Heterophoma poolensis (CBS 113.20). Tree topology of the ML analysis was similar to the MP. The best scoring RAxML tree with a final likelihood value of - 8386.622374 is presented. The matrix had 388 distinct alignment patterns, with 11.83% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.245798, C = 0.237676, G = 0.273178, T = 0.243348; substitution rates AC = 1.882600, AG = 4.123164, AT = 2.015920, CG = 0.907833, CT = 12.626910, GT = 1.000000; gamma distribution shape parameter a = 1.105097. RAxML bootstrap support values C 50% and Bayesian posterior probabilities C 0.95 (BYPP) are shown respectively near the nodes. Ex-type strains are in bold 123 Morphological based identification and diversity Fungal Diversity Fig. 32 Phylogenetic tree generated from Bayesian analysis based on combined ACT, tef1, GPD and TS sequence data for the genus Verticillium. Sixteen strains are included in the combined genes sequence analyses which comprise total of 2597 characters (609 characters for the ACT, 620 characters for tef1, 744 characters for GPD, 624 characters for TS) after alignment. For the Bayesian analysis, two parallel runs with six chains were run for 1,000,000 generations and trees were sampled every 100th generation, resulted in 20,002 trees from two runs of which 15,002 trees were used to calculate the posterior probabilities (each run resulted in 10,001 trees of which 7501 trees were sampled). Bootstrap support values for maximum likelihood (ML, first set) and maximum parsimony (MP, second set) greater than 75% and Bayesian posterior probabilities greater than 0.95 are indicated above or below the nodes. Ex-type strains are in bold. The tree is rooted with Gibellulopsis nigrescens (PD596) species, V. albo-atrum, V. alfalfae, V. dahliae, V. isaacii, V. klebahnii, V. longisporum, V. nonalfalfae, V. nubilum, V. tricorpus and V. zaregamsianum, were accepted within Verticillium sensu stricto (Inderbitzin et al. 2011). No sexual states are known. Descriptions and a key to these ten species were provided by Inderbitzin et al. (2011). (RPB1), the cytochrome oxidase subunit III gene (cox3), the small ribosomal rRNA subunit (rns), NADH dehydrogenase subunit genes (nad1 and nad3) were used (Barbara and Clewes 2003; Pantou et al. 2005; Zare and Gams 2008, 2016). Molecular based identification and diversity The first phylogenetic analysis of Verticillium species was made by Morton et al. (1995) to analysis the relationship between V. alboatrum and V. dahliae based on the internal transcribed spacer regions and intervening 5.8S rDNA (ITS) sequences data (Fig. 32, Table 22). Subsequently, SSU, LSU, RNA polymerase II largest subunit gene Recommended genetic marker (genus level)—LSU Recommended genetic marker (species level)—ITS Accepted number of species: 10 species. References: Inderbitzin et al. 2011 (morphology and phylogeny); Barbara and Clewes 2003, Morton et al. 1995, Pantou et al. 2005, Zare and Gams 2008, 2016 (phylogeny); Fradin and Thomma 2006, Blum et al. 2018 (pathogenicity) 123 Fungal Diversity Table 21 Details of the Stagonosporopsis isolates used in the phylogenetic analyses Species Stagonosporopsis actaeae Culture LSU GenBank Accession numbers ITS RPB2 TUB2 CBS 106.96* GU238166 GU237734 KT389672 CBS 114303 KT389760 KT389544 – KT389847 MFLUCC 16-1439* KY100874 KY100872 KY100876 KY100878 S. ajacis CBS 177.93* GU238168 GU237791 KT389673 GU237673 S. andigena CBS 269.80 GU238170 GU237817 – GU237675 CBS 101.80 GU238169 GU237714 – GU237674 S. artemisiicola S. astragali CBS 102636 CBS 178.25 GU238171 GU238172 GU237728 GU237792 KT389674 – GU237676 GU237677 S. caricae CBS 248.90 GU238175 GU237807 – GU237680 CBS 282.76 GU238177 GU237821 – GU237682 CBS 500.63 GU238190 GU237871 – GU237695 CBS 137.96 GU238191 GU237783 – GU237696 S. crystalliniformis CBS 713.85* GU238178 GU237903 KT389675 GU237683 S. cucurbitacearum CBS 133.96 GU238181 GU237780 KT389676 GU237686 S. dennisii CBS 631.68* GU238182 GU237899 KT389677 GU237687 S. ailanthicola S. chrysanthemi GU237671 S. dorenboschii CBS 426.90* GU238185 GU237862 KT389678 GU237690 S. helianthi CBS 200.87* KT389761 KT389545 KT389683 KT389848 S. heliopsidis CBS 109182 GU238186 GU237747 KT389679 GU237691 S. hortensis CBS 104.42 GU238198 GU237730 KT389680 GU237703 CBS 572.85 GU238199 GU237893 KT389681 GU237704 S. inoxydabilis CBS 425.90* GU238188 GU237861 KT389682 GU237693 S. loticola S. lupini CBS 562.81* CBS 101494* GU238192 GU238194 GU237890 GU237724 KT389684 KT389685 GU237697 GU237699 S. oculohominis CBS 634.92* GU238196 GU237901 KT389686 GU237701 S. pini MFLUCC 18-1549* MK348019 MK347800 MK434860 – S. rudbeckiae CBS 109180 GU238197 GU237745 – GU237702 S. tanaceti CBS 131484* JQ897461 NR_111724 – JQ897496 S. trachelii CBS 379.71 GU238173 GU237850 KT389687 GU237678 CBS 384.68 GU238174 GU237856 – GU237679 – S. valerianellae 123 CBS 273.92 GU238200 GU237819 CBS 329.67* GU238201 GU237832 GU237705 GU237706 Fungal Diversity Table 22 GenBank accession numbers of Verticillium isolates included in this study Taxa Strains Verticillium albo-atrum V. alfalfa ACT tef1 GPD TS PD747 JN188144 JN188272 JN188208 JN188080 PD489 JN188097 JN188225 JN188161 JN188033 V. dahlia PD322 HQ206921 HQ414624 HQ414719 HQ414909 V. isaacii PD660 HQ206985 HQ414688 HQ414783 HQ414973 V. klebahnii PD401 JN188093 JN188221 JN188157 JN188029 V. longisporum PD348 a1 HQ206930 HQ414633 HQ414728 HQ414918 V. longisporum PD348 d1 HQ206931 HQ414634 HQ414729 HQ414919 V. longisporum PD356 a1 HQ206934 HQ414637 HQ414732 HQ414922 V. longisporum PD356 d2 HQ206935 HQ414638 HQ414733 HQ414923 V. longisporum PD687 a1 HQ206993 HQ414696 HQ414791 HQ414981 V. longisporum PD687 d2 HQ206994 HQ414697 HQ414792 HQ414982 V. nonalfalfae PD592 JN188099 JN188227 JN188163 JN188035 V. nubilum PD742 JN188139 JN188267 JN188203 JN188075 V. tricorpus PD690 JN188121 JN188249 JN188185 JN188057 V. zaregamsianum PD736 JN188133 JN188261 JN188197 JN188069 Acknowledgements This work was funded by the grants of the project of National Natural Science Foundation of China (No. 31560489), Talent project of Guizhou science and technology cooperation platform ([2017]5788-5) and Guizhou science, technology department international cooperation base project ([2018]5806). 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’’ (Grant No. DBG6080013), Thailand Research Fund (TRF) grant no RSA5980068 entitled Biodiversity, phylogeny and role of fungal endophytes on above parts of Rhizophora apiculata and Nypa fruticans and‘‘Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion’’ (RDG6130001). Rajesh Jeewon would like to thank Mae Fah Luang University and the University of Mauritius for research support. Alan J.L. Phillips acknowledges the support from Biosystems and Integrative Sciences Institute (BioISI, FCT/UID/ Multi/04046/2013). References Adams GC, Wingfield MJ, Common R, Roux J (2005) Phylogenetic relationships and morphology of Cytospora species and related teleomorphs (Ascomycota, Diaporthales, Valsaceae) from Eucalyptus. 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