One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26-50 (2019

Ruvishika S Jayawardena

This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporiopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.

Novel species of fungi described in the present study include the following from Australia: Neoseptorioides eucalypti gen. & sp. nov. from Eucalyptus radiata leaves, Phytophthora gondwanensis from soil, Diaporthe tulliensis from rotted stem ends of Theobroma cacao fruit, Diaporthe vawdreyi from fruit rot of Psidium guajava, Magnaporthiopsis agrostidis from rotted roots of Agrostis stolonifera and Semifissispora natalis from Eucalyptus leaf litter. Furthermore, Neopestalotiopsis egyptiaca is described from Mangifera indica leaves (Egypt), Roussoella mexicana from Coffea arabica leaves (Mexico), Calonectria monticola from soil (Thailand), Hygrocybe jackmanii from littoral sand dunes (Canada), Lindgomyces madisonensis from submerged decorticated wood (USA), Neofabraea brasiliensis from Malus domestica (Brazil), Geastrum diosiae from litter (Argentina), Ganoderma wiiroense on angiosperms (Ghana), Arthrinium gutiae from the gut of a grasshopper (India), Pyrenochaeta telephoni from the screen of a mobile phone (India) and Xenoleptographium phialoconidium gen. & sp. nov. on exposed xylem tissues of Gmelina arborea (Indonesia). Several novelties are introduced from Spain, namely Psathyrella complutensis on loamy soil, Chlorophyllum lusitanicum on nitrified grasslands (incl. Chlorophyllum arizonicum comb. nov.), Aspergillus citocrescens from cave sediment and Lotinia verna gen. & sp. nov. from muddy soil. Novel foliicolous taxa from South Africa include Phyllosticta carissicola from Carissa macrocarpa, Pseudopyricularia hagahagae from Cyperaceae and Zeloasperisporium searsiae from Searsia chirindensis. Furthermore, Neophaeococcomyces is introduced as a novel genus, with two new combinations, N. aloes and N. catenatus. Several foliicolous novelties are recorded from La Réunion, France, namely Ochroconis pandanicola from Pandanus utilis, Neosulcatispora agaves gen. & sp. nov. from Agave vera-cruz, Pilidium eucalyptorum from Eucalyptus robusta, Strelitziana syzygii from Syzygium jambos (incl. Strelitzianaceae fam. nov.) and Pseudobeltrania ocoteae from Ocotea obtusata (Beltraniaceae emend.). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Dothideomycetes is one of the largest and most diverse class of ascomycetes. Its members are reported from many plant parts, but less has been reported from wild seed pods and fruits. Dothideomycetes can be seed-borne or colonize fruits and seed pods when they fall to the ground. We studied the Dothideomycetes found on wild fruits and seed pods, mainly in Thailand (tropical), and to a lesser extent, in China (temperate) and UK (temperate). We describe eight new genera, 50 new species, provide 38 new host records and propose seven new combinations. The new genera are: Amorocoelophoma (Amorosiaceae),

One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26–50 (2019) Ruvishika S. Jayawardena, Kevin D. Hyde, Rajesh Jeewon, Masoomeh Ghobad-Nejhad, Dhanushka N. Wanasinghe, NingGuo Liu, et al. Fungal Diversity An International Journal of Mycology ISSN 1560-2745 Volume 94 Number 1 Fungal Diversity (2019) 94:41-129 DOI 10.1007/s13225-019-00418-5 1 23 Your article is protected by copyright and all rights are held exclusively by School of Science. This e-offprint is for personal use only and shall not be self-archived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com”. 1 23 Author's personal copy Fungal Diversity (2019) 94:41–129 https://doi.org/10.1007/s13225-019-00418-5 (0123456789().,-volV)(0123456789(). ,- volV) One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26–50 (2019) Ruvishika S. Jayawardena1,2 • Kevin D. Hyde1,2,3 • Rajesh Jeewon4 • Masoomeh Ghobad-Nejhad5 • Dhanushka N. Wanasinghe3,6 • NingGuo Liu2,16 • Alan J. L. Phillips7 • José Ribamar C. Oliveira-Filho8 • Gladstone A. da Silva8 • Tatiana B. Gibertoni8 • P. Abeywikrama2,9 • L. M. Carris10 • K. W. T. Chethana2,9 • A. J. Dissanayake2 • S. Hongsanan11 • S. C. Jayasiri2 • A. R. McTaggart12 • R. H. Perera2 • K. Phutthacharoen2 K. G. Savchenko13 • R. G. Shivas14 • Naritsada Thongklang2 • Wei Dong2,15 • DePing Wei2,15 • Nalin N. Wijayawardena2 • Ji-Chuan Kang1 • Received: 17 October 2018 / Accepted: 16 January 2019 / Published online: 14 February 2019 Ó School of Science 2019 Abstract This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi. It focuses on 25 phytopathogenic genera: Alternaria, Bipolaris, Boeremia, Botryosphaeria, Calonectria, Coniella, Corticiaceae, Curvularia, Elsinoe, Entyloma, Erythricium, Fomitiporia, Fulviformes, Laetisaria, Limonomyces, Neofabraea, Neofusicoccum, Phaeoacremonium, Phellinotus, Phyllosticta, Plenodomus, Pseudopyricularia, Tilletia, Venturia and Waitea, using recent molecular data, up to date names and the latest taxonomic insights. For each genus a taxonomic background, diversity aspects, species identification and classification based on molecular phylogeny and recommended genetic markers are provided. In this study, varieties of the genus Boeremia have been elevated to species level. Botryosphaeria, Bipolaris, Curvularia, Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries, as many new species have been introduced to these genera. Keywords Boeremia DNA barcodes Endophytes Plant pathology Systematics Taxonomy Contents and contributors (main contributors underlined) 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. Alternaria–NG Liu, DN Wanasinghe Boeremia–SC Jayasiri, RS Jayawardena, KD Hyde Calonectria–RH Perera Coniella–KWT Chethana, NN Wijayawardena Corticiaceae–M Ghobad-Nejhad Elsinoe–RS Jayawardena, KD Hyde Entyloma–KG Savchenko, LM Carris Erythricium–M Ghobad-Nejhad Fomitiporia–N Thongklang Fulvifomes–JRC Oliveira-Filho, GA da Silva, TB Gibertoni Laetisaria–M Ghobad-Nejhad Limonomyces–M Ghobad-Nejhad & Ji-Chuan Kang jckang@gzu.edu.cn 38. Neofabraea–K Phutthacharoen 39. Phaeoacremonium– DP Wei, W Dong, R Jeewon 40. Phellinotus–JRC Oliveira-Filho, GA da Silva, TB Gibertoni 41. Plenodomus–DN Wanasinghe 42. Pseudopyricularia–NG Liu 43. Tilletia–AR McTaggart, RG Shivas 44. Venturia–S Hongsanan 45. Waitea–M Ghobad-Nejhad Updated genera 46. 47. 48. 49. 50. Botryosphaeria–AJ Dissanayake, AJL Philips Bipolaris–DN Wanasinghe Curvularia–DN Wanasinghe Neofusicoccum–AJL Philips Phyllosticta–P Abeywikrama, AJL Philips Extended author information available on the last page of the article 123 Author's personal copy 42 Introduction Fungi exhibit different types of associations with plants including endophytism, parasitism, saprotrophy and symbiosis (Dissanayake et al. 2018; Jayawardena et al. 2018). Phytopathogenic fungi can cause significant economic loss by reducing the quantity and the quality of crops (Chethana et al. 2017). Studies of systematics, biology and control of phytopathogenic fungi have a long, rich and diverse background (Maharachchikumbura et al. 2011; Udayanga et al. 2011, 2014a; Hyde et al. 2014; Jayawardena et al. 2015, 2016a; Dissanayake et al. 2016, 2017), but understanding has not been easy due to taxonomic inconsistencies leading to species identification problems. Morphological characters may overlap, making precise identification problematic. Therefore, there is a need to reevaluate the old names that were introduced based on morphology alone (Hyde et al. 2018b). Most of the biotrophs cannot be cultured under laboratory conditions, and many plant pathogenic fungi fail to produce sexual morphs (Dissanayake et al. 2018; Hyde et al. 2018a; Jayawardena et al. 2018), thus posing further problems for their identification. The biology of most phytopathogenic fungi remains poorly understood. The emergence of DNA sequences has provided better taxonomic insights on phytopathogenic fungi (Cannon et al. 2012; Wingfield et al. 2012; Manamgoda et al. 2013; Udayanga et al. 2013; Hyde et al. 2014; Nilsson et al. 2014). Based on DNA sequence analyses, many phytopathogenic fungal genera have been reported to be polyor paraphyletic and several fungal species (e.g. Colletotrichum and Diaporthe) form species complexes (Hyde et al. 2014; Udayanga et al. 2014b; Jayawardena et al. 2016b). Phytopathogens are important in global plant trade and in implementation of disease management strategies. Therefore, addressing taxonomic confusion and accurate species identification are extremely important. In 2014 we published One Stop Shop I (Hyde et al. 2014), with a plan to continue the series with follow up papers. The present publication is the second in the series providing updated phylogenetic backbone trees of phytopathogenic genera using recent molecular data, recommendations of correct names and latest taxonomic notes. Materials and methods 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 was carried out by using the default settings of 123 Fungal Diversity (2019) 94:41–129 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) as well as manual adjustments where necessary. Maximum parsimony analysis (MP) was performed using PAUP (Phylogenetic Analysis Using Parsimony) v. 4.0b10 (Swofford 2002) to obtain the most parsimonious trees. Gaps were treated as missing data and ambiguously aligned regions were excluded. Trees were inferred using the heuristic search option with tree bisection reconnection branch swapping and 1000 random sequence additions. Maxtrees were set up to 5000, branches of zero length were collapsed and all multiple parsimonious trees were saved. Descriptive tree statistics for parsimony (tree length, consistency index, retention index, rescaled consistency index, and homoplasy index) were calculated for trees generated under different optimal criteria. The robustness of the most parsimonious trees was evaluated by 1000 bootstrap replications resulting from maximum parsimony analysis (Hillis and Bull 1993). Kishino-Hasegawa tests (Kishino and Hasegawa 1989) were performed in order to determine whether trees were significantly different. Maximum likelihood analyses were also performed in raxmlGUIv.0.9b2 (Silvestro and Michalak 2012). Rapid bootstrapping with 1000 non parametric bootstrapping iterations, using the general time reversible model (GTR) with a discrete gamma distribution, was set as the search strategy. Bayesian inference (BI) was used in addition to construct the phylogenies using Mr. Bayes v.3.1.2 (Ronquist and Huelsenbeck 2003). MrModeltest v. 2.3 (Nylander et al. 2004) was used for statistical selection of best-fit model of nucleotide substitution and was incorporated into the analyses. Results Taxonomic details pertaining to classification, species identification and numbers, molecular phylogeny, and recommended genetic markers are summarized and provided for 25 important phytopathogenic genera. Classification follows Wijayawardene et al. (2018) and guidelines for new species recognition based on molecular data follow Jeewon and Hyde (2016). Alternaria Nees, Syst. Pilze (Würzburg): 72 (1816) [1816–17] For synonyms see Index Fungorum (2019) Background Alternaria was established by Nees von Esenbeck (1816) and species of Alternaria are known as serious plant pathogens (Nishimura et al. 1978; Peever et al. 2002; Author's personal copy Fungal Diversity (2019) 94:41–129 Thomma 2003; Lawrence et al. 2013; Woudenberg et al. 2013, 2015) and saprobes (Wanasinghe et al. 2018). Alternaria species have been also recorded as endophytes in grasses, angiosperms, rice and other herbaceous plants and shrubs (Fisher and Petrini 1992; Schulz et al. 1993; Rosa et al. 2009; Polizzotto et al. 2012) and they have been also isolated from soil (Hong and Pryor 2004). Many Alternaria species are saprobic on a variety of plant tissues in different habitats (Thomma 2003; Liu et al. 2015; Wanasinghe et al. 2018). Some Alternaria species, such as A. alternata, produce host-specific toxins (Hyde et al. 2018a). Several taxa are also important postharvest pathogens, e.g. A. alternata and A. solani (El-Goorani and Sommer 1981; Reddy et al. 2000), or airborne allergens causing upper respiratory tract infections and asthma in humans (Mitakakis et al. 2001; Woudenberg et al. 2015; Hyde et al. 2018a). Mycotoxins produced by Alternaria have been found in many crops including grapevine, olive, orange and tomato. This genus has been considered as one of the most important phytopathogens, especially in temperate regions (Ariyawansa et al. 2015a, b; Wanasinghe et al. 2018). Classification—Dothideomycetes, Pleosporomycetidae, Pleosporales, Pleosporaceae Type species—Alternaria alternata (Fr.) Keissl., Beih. bot. Zbl., Abt. 2 29: 434 (1912) Distribution—Worldwide Disease symptoms—Leaf blotch, leaf spot, stem canker and stem end rots Alternaria generally infects the aerial parts of its host. On leafy vegetables the infection typically starts as a small, circular, dark spot. As the disease progresses, the circular spots may enlarge and are usually gray, gray-tan or near black in colour. In some cases the spots may develop in a target pattern of concentric rings and if the host leaves are large enough unrestricted symptom development can be observed. The lesion may often be covered with a fine, black, fuzzy growth (Agrios 1997). On roots, tubers, stems and fruits dark brown to black sunken lesions with concentric rings may occur. Lesions enlarge and may girdle the stem, eventually killing the plant. Fruits that are harvested from infested plants have brown or black necrotic sunken lesions (Agrios 1997; Wenneker et al. 2017). The above symptoms can be observed when the infection is caused by A. alternata, A. arborenses, A. tenuissima (Diskin et al. 2017). Alternaria brassicola produces black sooty coloured spores within the leaf spot (Kreis et al. 2016). Purple blotch disease of Allium sp. is caused by A. porri, which initially appears as small whitish necrotic lesions on leaves, becoming large, sunken and subsequently turning brown and dark (Hahuly et al. 2018). 43 Hosts—Has a wide range of hosts including the families Amarylidaceae, Apiaceae, Brassicaceae, Fabaceae, Lamiaceae, Rosaceae, Rutaceae, Solanaceae, Vitaceae plus many ornamental plants and a number of weeds (Farr and Rossman 2019). Morphological based identification and diversity The asexual morphs of Alternaria are ubiquitous in different environments and characterized by distinct, single, simple or irregular, loosely branched, solitary conidiophores, which may be in fascicles, and by the production of dark coloured phaeodictyospores in chains, the conidia often having a beak of tapering apical cells (Woudenberg et al. 2013). Sexual morphs have small, globose to ovoid, dark brown, papillate ostiolate ascomata, mostly 8-spored, bitunicate asci with a pedicel and ocular chamber, and muriform ascospores (e.g. section Crivellia, Eureka, Infectoria; Woudenberg et al. 2013; Ariyawansa et al. 2015a; Wanasinghe et al. 2018). Neergaard (1945) divided Alternaria into three major sections, Brevicatenatae, Longicatenatae and Noncatenatae, based on conidial catenation. However, this division is unreliable as catenation is affected by growth conditions. Simmons (1992, 1995) arranged several species groups within Alternaria based on the morphological similarity among species,. Some other genera, such as Stemphylium (Wallroth 1833) and Ulocladium (Preuss 1851) also produce phaeodictyosporic conidia and are morphologically similar to Alternaria, and this has further led to taxonomic complications. Simmons (2007) revised Alternaria taxonomy based on morphology and 275 species were recognized. At the same time, Simmons (2007) proposed three new genera Alternariaster, Chalastospora and Teretispora, for some species that were previously described in Alternaria. The Alternaria complex currently comprises 24 sections and six monophyletic lineages (Woudenberg et al. 2013). Colony and conidial morphology are the primary characters to identify species within this genus (Ellis 1971, 1976; Simmons 1992). Conidia in some sections are mostly dictyosporous, e.g. Alternata and Japonicae, while some are mostly phragmosporous, e.g. Alternantherae and Nimbya. Species in some sections have long apical narrow beaks or secondary conidiophores, e.g. Alternantherae, Dianthicola and Porri, while such characters are absent in other sections, e.g. Chalastospora, Gypsophilae and Ulocladium. However, in some sections overlapping conidial morphology is observed, which makes identification of Alternaria based on morphology challenging. For example, dictyospores and phragmospores can be found in the same section, such as Infectoriae and Phragmosporae. 123 Author's personal copy 44 Therefore, the use of DNA sequence data is very important in resolving Alternaria taxonomy. Molecular based identification and diversity Molecular phylogeny has revealed multiple polyphyletic taxa within Alternaria and Alternaria species clades, which do not always correlate to morphological species-groups (Inderbitzin et al. 2006; Runa et al. 2009; Lawrence et al. 2012). Pryor and Gilbertson (2000) elucidated relationships among Alternaria, Stemphylium and Ulocladium based on ITS and SSU sequence data and revealed that Stemphylium species were phylogenetically distinct from Alternaria and Ulocladium species. Most Alternaria and Ulocladium clustered together in a large Alternaria/Ulocladium clade (Pryor and Gilbertson 2000). Chou and Wu (2002) confirmed that filament-beaked Alternaria species constitute a monophyletic group distinct from the other members in this genus and hypothesized that this group is evolutionary distinct based on ITS sequence based phylogenies. Two new species groups, A. panax and A. gypsophilae were introduced by Lawrence et al. (2013) with phylogenetic evidence, and they accepted eight well supported asexual species-sections within Alternaria, while the taxa with known sexual morphs, the A. infectoria species-groups, were not given similar rank. Woudenberg et al. (2013) delineated taxa within Alternaria and allied genera based on SSU, LSU, ITS, GAPDH, RPB2 and TEF1-a sequence data. The generic circumscription of Alternaria was emended and 24 internal clades in the Alternaria complex were treated as sections, together with six monotypic lineages. Ariyawansa et al. (2015a) revised the classification of Pleosporaceae with a major focus on Alternaria and allied genera. Agreeing with Woudenberg et al. (2013), six monotypic lineages and 24 internal clades were recognized, with Xenobotryosphaeria clustering within A. infectoria. The present study reconstructs the phylogeny of Alternaria based on analyses of a combined SSU, LSU, RPB2, ITS, GAPDH and TEF1-a sequence data (Table 1, Fig. 1). The phylogenetic tree is updated with recently introduced Alternaria species, and the resulting tree corresponds to previous studies (Woudenberg et al. 2013; Ariyawansa et al. 2015a; Thambugala et al. 2017). Recommended genetic markers (Genus level)—LSU and SSU Recommended genetic markers (Species level)—ITS, GAPDH, RPB2 and TEF1-a GAPDH is the common species marker used in identification of Alternaria species. Combined GAPDH with ITS, RPB2 and TEF1-a provides satisfactory resolution for resolving species. Accepted number of species: There are 730 species epithets in Index Fungorum (2019) under this genus. However, 73 have DNA sequence data. 123 Fungal Diversity (2019) 94:41–129 References: Simmons (2007) (morphology), Ariyawansa et al. (2015a), Lawrence et al. (2013), Woudenberg et al. (2013, 2015) (morphology, phylogeny). Boeremia Aveskamp, Gruyter & Verkley, in Aveskamp, Gruyter, Woudenberg, Verkley & Crous, Stud. Mycol. 65: 36 (2010) Background Boeremia was established by Aveskamp et al. (2010) to accommodate phoma-like species that are morphologically similar to Phoma exigua. To date only B. lycopersici is reported to have a sexual morph (Chen et al. 2015). Classification—Dothideomycetes, Pleosporomycetidae, Pleosporales, Didymellaceae Type species—Boeremia exigua (Desm.) Aveskamp, Gruyter & Verkley, in Aveskamp, Gruyter, Woudenberg, Verkley & Crous, Stud. Mycol. 65: 37 (2010) Distribution—Worldwide Disease Symptoms—Black node, Bulb rot, Canker, Leaf spots, Stem rot, Shoot dieback, Tan spot All foliar parts of a plant can be affected. Dark brown sunken lesions form at the base of the plant and eventually expand to girdle the stem, resulting in yellowing and wilting of the older leaves. This will lead to the death of the plant. Fruit infection starts as a water soaked lesion that progress rapidly into a sunken brown/black/gray lesion with concentric rings. Leaf lesions begin as small spots that develop into brown/gray lesions with concentric rings (Jones et al. 2011; Zhao et al. 2016). Hosts—Amaryllidaceae, Apocynaceae, Araliaceae, Caprifoliaceae, Chenopodiaceae, Crassulaceae, Fabaceae, Lamiaceae, Linaceae, Oleaceae, Rubiaceae, Salicaceae, Solanaceae, Ulmaceae and Umbelliferae (Farr and Rossman 2019). Morphological based identification and diversity This genus is characterized by variable conidial shape, aseptate to 2-septate conidia in the asexual morph and a sexual morph with ellipsoidal, 1-septate ascospores. Index Fungorum lists 13 species and 12 varieties of Boeremia exigua (Index Fungorum 2019). Naming of species of Boeremia and varieties of B. exigua is mainly based on host association (Aveskamp et al. 2010; Jayasiri et al. 2017). Some B. exigua varieties and Boeremia sp. are hostspecific, while others seem to have a very broad host range. Original epithets of Boeremia (and Phoma) species and varieties were based on the hosts from which they were collected and later, characters from artificial culture media were used (Boerema et al. 2004). Molecular phylogenetics has only recently been employed to separate these taxa and this has often necessitated renaming (Aveskamp et al. 2010). Thus, nomenclature is still confused (Berner et al. 2015). Author's personal copy Fungal Diversity (2019) 94:41–129 45 Table 1 Alternaria. Details of the isolates used in the phylogenetic analyses Species Isolate SSU LSU RPB2 ITS GAPDH TEF1 Alternaria alternantherae CBS 124392 KC584506 KC584251 A. alternariae CBS 126989* KC584604 KC584346 KC584374 KC584179 KC584096 KC584633 KC584470 AF229485 AY278815 A. alternata MFLUCC 14–1185 KP334722 KP334702 KP334738 KP334712 KC584730 A. alternata CBS 916.96* KC584507 DQ678082 KC584375 AF347031 A. alternata MFLUCC 14-1184 KP334721 KP334701 KP334737 KP334711 AY278808 KC584634 A. anigozanthi CBS 121920* KC584508 KC584252 KC584376 KC584180 KC584097 KC584635 A. aspera CBS 115269* KC584607 KC584349 KC584474 KC584242 KC584166 KC584734 A. bornmuelleri DAOM 231361* KC584624 KC584366 KC584491 FJ357317 FJ357305 KC584751 A. botryospora CBS 478.908* KC584594 KC584336 KC584461 AY278844 AY278831 KC584720 A. botrytis CBS 197.67* KC584609 KC584351 KC584476 KC584243 KC584168 KC584736 A. brassicicola A. caricis CBS 118699 CBS 480.90* KC584515 KC584600 KC584259 KC584342 KC584383 KC584467 JX499031 AY278839 KC584103 AY278826 KC584642 KC584726 KC584386 KC584188 KC584106 A. carotiincultae CBS 109381* KC584518 KC584262 A. cesenica MFLUCC 13–0450* KP711385 KP711384 KP711383 KC584645 KP711386 A. cetera CBS 121340* KC584573 KC584317 KC584441 JN383482 AY562398 A. cheiranthi CBS 109384 KC584519 KC584263 KC584387 AF229457 KC584107 KC584646 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 KC584699 A. conjuncta CBS 196.86* KC584522 KC584266 KC584390 FJ266475 AY562401 KC584649 A. cumini CBS 121329* KC584523 KC584267 KC584391 KC584191 KC584110 KC584650 KY703616 A. dactylidicola MFLUCC 15–0466* KY703618 KY703617 KY750720 A. dauci CBS 117097 KC584524 KC584268 KC584392 KC584192 KC584111 KC584651 A. daucifolii CBS 118812* KC584525 KC584269 KC584393 KC584193 KC584112 KC584652 A. dianthicola CBS 116491 KC584526 KC584270 KC584394 KC584194 KC584113 KC584653 A. didymospora CBS 766.79 KC584588 KC584330 KC584455 FJ357312 FJ357300 KC584714 A. doliconidium A. elegans KUMCC 17-0263* CBS 109159* MG829094 KC584527 MG828980 KC584271 KC584395 MG828864 KC584195 KC584114 KC584654 A. embellisia CBS 339.71 KC584582 KC584324 KC584449 KC584230 KC584155 KC584708 A. ethzedia CBS 197.86* KC584530 KC584274 KC584398 AF392987 AY278795 KC584657 KC584456 JN383490 JN383471 KC584715 KC584118 KC584660 A. eureka CBS 193.86* KC584589 KC584331 A. forlicesenensis MFLUCC 13–0456* KY769659 KY769658 KY769657 A. gypsophilae CBS 107.41 KC584533 KC584277 KC584401 KC584199 A. hampshirensis MFLUCC 17-0783 MG829096 MG828982 MG829247 MG828866 A. hyacinthi CBS 416.71* KC584590 KC584332 KC584457 KC584233 KC584158 KC584716 KC584662 A. infectoria CBS 210.86* KC584536 KC584280 KC584404 DQ323697 AY278793 A. japonica CBS 118390 KC584537 KC584281 KC584405 KC584201 KC584121 KC584663 A. juxtiseptata CBS 119673* KC584538 KC584282 KC584406 KC584202 KC584122 KC584664 A. leucanthemi CBS 421.65* KC584605 KC584347 KC584472 KC584240 KC584164 KC584732 A. leucanthemi CBS 422.65 KC584606 KC584348 KC584473 KC584241 KC584165 KC584733 A. longipes CBS 540.94 KC584541 KC584285 KC584409 AY278835 AY278811 KC584667 A. longipes A. multiformis MFLUCC 16–0592 CBS 102060* KY038355 KC584617 KY000658 KC584359 KY056664 KC584484 KY026585 FJ266486 KC584174 KY542121 KC584744 A. murispora MFLU 14-0758* KP334724 KP334704 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. obovoidea CBS 101229 KC584618 KC584360 KC584485 FJ266487 FJ266498 KC584745 NR_137964 123 Author's personal copy 46 Fungal Diversity (2019) 94:41–129 Table 1 (continued) Species Isolate SSU LSU RPB2 ITS GAPDH TEF1 A. oregonensis CBS 542.94* KC584548 KC584292 KC584416 FJ266478 FJ266491 KC584674 A. oudemansii CBS 114.07* KC584619 KC584361 KC584486 FJ266488 KC584175 KC584746 A. panax CBS 482.81 KC584549 KC584293 KC584417 KC584209 KC584128 KC584675 A. papavericola CBS 116606* KC584579 KC584321 KC584446 FJ357310 FJ357298 KC584705 A. penicillata CBS 116608* KC584572 KC584316 KC584440 FJ357311 FJ357299 KC584698 A. penicillata CBS 116607* KC584580 KC584322 KC584447 KC584229 KC584153 KC584706 A. perpunctulata CBS 115267* KC584550 KC584294 KC584418 KC584210 KC584129 KC584676 A. photistica A. phragmospora CBS 212.86 CBS 274.70* KC584552 KC584595 KC584296 KC584337 KC584420 KC584462 KC584212 JN383493 KC584131 JN383474 KC584678 KC584721 A. planifunda CBS 537.83* KC584596 KC584338 KC584463 FJ357315 FJ357303 KC584722 A. poaceicola MFLUCC 13–0346* KY038357 KY205718 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. saponariae CBS 116492 KC584557 KC584301 KC584425 KC584215 KC584135 KC584683 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. simsimi CBS 115265* KC584560 KC584304 KC584428 JF780937 KC584137 KC584686 A. solani CBS 116651 KC584562 KC584306 KC584430 KC584217 KC584139 KC584688 A. solidaccana CBS 118698* KC584564 KC584308 KC584432 KC584219 KC584141 KC584690 A. sonchi Alternaria sp. CBS 119675 CBS 115.44 KC584565 KC584556 KC584309 KC584300 KC584433 KC584424 KC584220 KC584214 KC584142 KC584134 KC584691 KC584682 A. subcucurbitae CBS 121491* KC584622 KC584364 KC584489 KC584249 EU855803 KC584749 A. tagetica CBS 479.81 KC584566 KC584310 KC584434 KC584221 KC584143 KC584692 A. tellustris CBS 538.83* KC584598 KC584340 KC584465 FJ357316 AY562419 KC584724 A. tenuissima CBS 918.96 KC584567 KC584311 KC584435 AF347032 AY278809 KC584693 A. terricola CBS 202.67* KC584623 KC584365 KC584490 FJ266490 KC584177 KC584750 A. tumida CBS 539.83* KC584599 KC584341 KC584466 FJ266481 FJ266493 KC584725 A. vaccariicola CBS 118714* KC584571 KC584315 KC584439 KC584224 KC584147 KC584697 Pyrenophora phaeocomes DAOM 222769 DQ499595 DQ499596 DQ497614 KY026587 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher stains are in bold Colony and conidial morphology are the primary characters to identify species within this genus. However, using these characters alone in identification can cause errors as these characters may overlap between species. Therefore, it is important to use DNA sequence data when identifying species of this genus (Chen et al. 2015, 2017; Marin-Felix et al. 2017). Molecular based identification and diversity Recent studies on the taxonomy of Boeremia have employed molecular methods to reveal the phylogenetic relationships among species (Aveskamp et al. 2010). Berner et al. (2015), Chen et al. (2015, 2017), Marin-Felix et al. (2017) and Jayasiri et al. (2017) revisited the genus and described new species. This study reconstructs the 123 phylogeny using a combined LSU, RPB2, ITS, TUB2 and TEF1-a sequence dataset (Table 2, Fig. 2). In this study, we elevate the varieties of B. exigua and change the status of ten species based on combined phylogenetic analysis as well as synonymise three varieties under B. exigua. Until further collections are found, herein we propose to keep CBS 119730 as Boeremia sp. Based on the multigene concatenated phylogenies we accept 22 species in this genus. Boeremia coffeae (Henn.) Jayasiri, Jayaward. & K.D. Hyde, comb. nov. IF555804 : Ascochyta coffeae Henn., Hedwigia 41: 307 (1902) : Boeremia exigua var. coffeae (Henn.) Aveskamp et al., Stud. Mycol. 65: 37 (2010) Author's personal copy Fungal Diversity (2019) 94:41–129 47 Fig. 1 Phylogenetic tree generated by maximum likelihood analysis of combined SSU, LSU, ITS, RPB2, GAPDH and TEF1-a sequence data of Alternaria species. Eighty strains are included in the analyses. The tree is rooted with Pyrenophora phaeocomes (DAOM 222769). Tree topology of the ML analysis was similar to the BI. The best scoring RAxML tree with a final likelihood value of - 24349.980578 is presented. The matrix had 1172 distinct alignment patterns, with 9.91% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.251668, C = 0.245757, G = 0.259668, T = 0.242908; substitution rates AC = 1.353890, AG = 4.605576, AT = 1.059439, CG = 0.801610, CT = 9.121730, GT = 1.000000; gamma distribution shape parameter a = 0.944898. RAxML bootstrap support values C 75% and Bayesian posterior probabilities C 0.95 (PP) are shown near the nodes. The scale bar indicates 0.02 changes per site. Ex-type (ex-epitype) strains are in bold 123 Author's personal copy 48 Fungal Diversity (2019) 94:41–129 Table 2 Boeremia. Details of the isolates used in the phylogenetic analyses Species Isolate LSU ITS RPB2 TUB2 TEF1 Boeremia coffeae CBS 109183; PD 2000/10506; IMI 300060 GU237943 GU237748 KT389566 GU237505 KY484678 B. crinicola CBS 109.79 GU237927 GU237737 KT389563 GU237489 – B. diversispora CBS 102.80 GU237930 GU237725 KT389565 GU237492 KY484676 B. exigua CBS 431.74; PD 74/2447 EU754183 FJ427001 KT389569 FJ427112 KY484687 CBS 119.38 KT389707 KT389490 – KT389784 – CBS 113.36 MH867235 KY484642 – KY484742 KY484683 CBS 534.75 MH872718 MH860950 – KY484746 KY484689 CBS 101197 GU237931 GU237718 KT389570 GU237493 KY484690 CBS 101213; PD 92/959 GU237932 GU237723 KT389571 GU237494 KY484692 CBS 100354; PD 83/448 GU237944 GU237711 KT389577 GU237506 – B. foveata B. galiicola CBS 109176; PD 94/1394 MFLUCC 15-0771* GU237946 KX698026 GU237742 KX698037 KT389578 – GU237508 KX698030 KY484714 – B. gilvescens CBS 101150*; PD 79/118 EU754182 GU237715 KT389568 GU237495 KY484694 B. hedericola CBS 367.91*; PD 87/229 GU237949 GU237842 KT389579 GU237511 KY484718 B. heteromorpha CBS 443.94* GU237935 GU237866 KT389573 GU237497 KY484700 CBS 101196; PD 79/176 GU237934 GU237717 KT389572 GU237496 KY484699 B. inoxydabilis CBS 372.75 MH872672 KY484656 – KY484754 KY484701 B. lilacis CBS 569.79; PD 72/741;IMI 331909 GU237936 GU237892 – GU237498 KY484721 CBS 588.67 KT389709 KT389492 – KT389786 – LC 5178 KY742201 KY742047 – KY742289 – LC 8116 KY742202 KY742048 – KY742290 – CBS 116.76*; ATCC 32332;IMI 197074; PD 75/544 GU237938 GU237754 KT389574 GU237500 KY484705 CBS 109.49 MH867998 MH856453 – KY484755 KY484702 CBS 248.38 KT389703 KT389486 KT389575 KT389780 – CBS 114.28 GU237937 GU237752 – GU237499 KY484704 B. lycopersici CBS 378.67; PD 67/276 GU237950 GU237848 KT389580 GU237512 KY484726 B. noackiana B. opuli CBS 100353; PD 87/718 LC 8117* GU237952 KY742199 GU237710 KY742045 – KY742133 GU237514 KY742287 KY484727 – LC 8118 KY742200 KY742046 KY742134 KY742288 – CBS 100167*; PD 93/217 GU237939 GU237707 – GU237501 KY484706 B. linicola B. populi B. pseudolilacis B. rhapontica CBS 101202 KY742199 KY742046 KY742133 KY742287 KY484709 CBS 101207*; PD 94/614 GU237941 GU237721 – GU237503 KY484710 – CBS 462.67 KT389705 KT389488 – KT389782 CBS 423.67 KT389704 KT389487 KT389576 KT389781 – CBS 113651* – KY484662 – KY484760 KY484713 B. sambuci-nigrae CBS 629.68*; CECT 20048;IMI 331913; PD 67/753 GU237955 GU237897 – GU237517 KY484734 B. strasseri CBS 126.93; PD 73/642 GU237956 GU237773 KT389584 GU237518 KY484735 B. telephii CBS 109175; PD 79/524 GU237958 GU237741 KT389585 GU237520 KY484737 B. trachelospermi CGMCC 3.18222* KY064032 KY064028 KY064033 KY064051 – Boeremia sp. CBS 119730 GU237942 GU237759 KT389567 GU237504 – Phoma herbarum CBS 615.75 EU754186 FJ427022 KP330420 KF252703 KR184186 Ex-type (ex-epitype) strains are in bold and marked with an * and reference strains are in bold Reference Strain: CBS 109183 (= reference specimen sensu Boerema et al. 2004; Aveskamp et al. 2010; Chen et al. 2015). For a complete description see de Gruyter et al. (2002). 123 This species was described from leaves of coffee plants as Ascochyta coffeae. Based on phylogenetic analyses, Aveskamp et al. (2010) placed this species in the Boeremia exigua species complex. In our phylogenetic analyses based on LSU, RPB2, ITS, TUB2 and TEF1-a, the Author's personal copy Fungal Diversity (2019) 94:41–129 49 Fig. 2 Phylogenetic tree inferred from a maximum likelihood analysis based on analyses of a concatenated alignment of LSU, ITS, RPB2, TUB and TEF1-a sequence data of 41 strains representing the genus Boeremia, which comprise 2746 characters including gaps. Tree is rooted with Phoma herbarum (CBS 615.75). Tree topology of the ML analysis was similar to the MP and BI (not shown). The best scoring RAxML tree with a final likelihood value of - 8078.423038 is presented. The matrix had 393 distinct alignment patterns, with 19.32% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.238158, C = 0.240395, G = 0.268922, T = 0.252525; substitution rates AC = 1.084080, AG = 2.823706, AT = 1.555532, CG = 0.936952, CT = 8.695282, GT = 1.000000; gamma distribution shape parameter a = 0.1000000000. The RAxML and MP bootstrap support values above 50% and Bayesian posterior probabilities above 0.90 are given near to each branch. The scale bar indicates 0.1 changes per site. The ex-type strains are in bold reference strain of this species is closely related with the type strain of B. rhapontica (Fig. 2). However, B. coffeae can be differentiated from B. rhapontica by smaller pycnidia (70–80 lm vs 4–6 lm) (de Gruyter et al. 2002; Berner et al. 2015). Aveskamp et al. (2010) listed two strains under this species, CBS 119730 and CBS 109183 even though they do not cluster together in the combined multigene analysis of LSU, ITS and TUB2. CBS 119730 123 Author's personal copy 50 strain was introduced by Stewart (1957) as Ascochyta tarda, the causal agent of coffee leaf blight and stem dieback. In the combined multigene analyses of Jayasiri et al. (2017) and this study the above mentioned two strains do not cluster together. When we compared the base pair differences among these two strains, we found that CBS 119730 has 1 bp, 9 bp and 5 bp differences in ITS, RPB2 and TUB2 regions respectively. CBS 119730 differs from B. coffeae in having larger pycnidia (70–110 lm vs 70–80 lm) and conidia (9–14 lm vs 50–199 lm). According to the original description, CBS 119730 has been observed to occur together with a Mycosphaerella sp., however, the connection between these species have not yet been proven. Therefore, here we assign CBS 109183 as the reference strain (= reference specimen sensu Ariyawansa et al. 2014) for this species and keep CBS 119730 as Boeremia sp. until further collection is found. Boeremia exigua (Desm.) Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010) IF515624 : Phoma exigua Desm. Annls Sci Nat Bot sér 3 11(2): 282(1849) = Boeremia exigua var. forsythia (Sacc.) Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010) = Boeremia exigua var. viburni (Roum. ex. Sacc.) Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010) Reference Strain: CBS 431.74 (= reference specimen sensu Boerema et al. 2004; Aveskamp et al. 2010; Chen et al. 2015). For a complete description see Aveskamp et al. (2010). This is the type species of the genus Boeremia. Boerema et al. (2004) assigned a reference strain (= reference specimen sensu Ariyawansa et al. 2014) for this species as CBS 431.74 and this was followed in the studies of Aveskamp et al. (2010), Chen et al. (2017) and Jayasiri et al. (2017). In the multigene phylogenetic analyses of this study, B. exigua var. forsythia and B. exigua var. vibruni clustered together with the reference strain of B. exigua (CBS 431.74). Sequences of B. exigua (CBS 431.74) and B. exigua var. forsythia (CBS 101213) are almost identical, with only 1 bp difference in each ITS and RPB2 gene regions. Between B. exigua and B. exigua var. vibruni (CBS 100354) we found only 1 bp difference in the RPB2 region. Therefore, in this study we synonymise B. exigua var. forsythia and B. exigua var. vibruni under B. exigua. Boeremia gilvescens (Aveskamp et al.) Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555805 : Boeremia exigua var. gilvescens Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010) 123 Fungal Diversity (2019) 94:41–129 Holotype: The Netherlands, Baarn, from leaves of Dactylis purpurea, 1970, H.A. van der Aa, CBS H-16281, ex-type culture CBS 761.70. For a complete description see Aveskamp et al. (2010). This species differs from B. exigua by having yellowish conidial matrix and absence of positive reaction to NaOH (Aveskamp et al. 2010). LSU, ITS and TUB2 sequences of B. exigua (CBS 471.34) and B. gilvescens (CBS 761.70) are almost identical. There are only 2 bp differences in RPB2. However, there are 41 bp differences in TEF1-a gene region. Boeremia heteromorpha (Schulzer & Sacc.) Jayaward., Jayasiri & K.D. Hyde, comb. nov. IF555806 : Phoma heteromorpha Schulzer & Sacc., Revue mycol., Toulouse 6(22): 74 (1884) : Phoma exigua var. heteromorpha (Schulzer & Sacc.) Noordel. & Boerema, Verslagen Meded. Plantenziektenk. Dienst Wageningen 166: 109 (1989) : Boeremia exigua var. heteromorpha (Schulzer & Sacc.) Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010) Neotype: Italy, Perugia, from Nerium oleander (Apocynaceae), deposited in CBS Aug. 1994, A. Zazzerini, HMAS246695; ex-neotype culture CBS 443.94. For a complete description see Chen et al. (2015). Chen et al. (2015) designate a neotype for Phoma heteromorpha. In the phylogenetic analyses of Chen et al. (2015) and in this paper (Fig. 2), this species clusters with B. populi and we were unable to identify any base pair differences among these two species. However, Chen et al. (2015) maintained these as two separate species as B. heteromorpha occurred on Nerium oleander and B. populi on Populus and Salix sp. respectively. Therefore, in this study we follow Chen et al. (2015) and maintain B. heteromorpha and B. populi as two distinct species. Boeremia inoxydabilis (Boerema & Vegh) Jayaward., Jaysiri & K.D. Hyde, comb. nov. IF555812 = Phoma exigua var. inoxydabilis Boerema & Vegh, in Vegh et al., Bull. Trimest. Soc. Mycol. Fr. 90(2): 130(1974) Reference Strain: CBS 372.75/ATCC 32161. Phoma exigua var. inoxydabilis was introduced to accommodate a taxon found on Vinca minor and V. major in Europe and North America (Vegh et al. 1974). Van der Aa (1973) mentioned that the French type culture PC 2198 has been lost. Aveskamp et al. (2010) mentioned that this variety may be identical to B. gilvescens. However, CBS 372.75 is closely related to B. pseudolilacis in the phylogenetic analyses (Fig. 2). The LSU sequence of strain CBS 372.75 is short and is identical with B. gilvescens and B. pseudolilacis. The same can be seen in the ITS gene region. There is one base pair difference in the TUB2 locus among Author's personal copy Fungal Diversity (2019) 94:41–129 these three strains. The TEF1-a sequence of CBS 372.75 is almost identical with B. pseudolilacis. There are 25 bp differences with B. gilvescens which makes it a different species from B. gilvescens. Here we elevate this taxon to B. inoxydabilis. Boeremia lilacis (Sacc.) Qian Chen & L. Cai, in Chen et al. Stud. Mycol. 82:170 (2015) IF515629 : Phoma herbarum f. lilacis Sacc., Michelia 2(1):93 (1880) : Phoma exigua var. lilacis (Sacc.) Boerema, Phytopath. Mediterr. 18:106 (1979) : Boeremia exigua var. lilacis (Schulzer & Sacc.) Aveskamp, Gruyter & Verkley, in Aveskamp et al., Stud. Mycol. 65: 38 (2010) Reference Strain: CBS 569.79 (= reference specimen sensu Berner et al. 2015; Chen et al. 2015). For a complete description see Chen et al. (2015). Chen et al. (2015) elevated this taxon to species level based on the multigene phylogeny in Berner et al. (2015). In our multigene phylogenetic analysis we identified CBS 588.67, CBS 569.79, LC 8116 and LC 5178 as B. lilacis. However, CBS 588.67, LC 8116 and LC 5178 lack TEF1-a sequence data and the LSU sequences are shorter (964 bp) than the type strain CBS 569.79. This may be the reason for these four strains do not cluster together. However, further collection and sequence data are needed for clarification. Until then, we treat CBS 588.67, LC 8116 and LC 5178 as B. lilacis. Boeremia linicola (Naumov & Vassilijevsky) Jayaward., Jayasiri & K.D. Hyde comb. nov. IF555807 : Ascochyta linicola Namov & Vassilijecsky, Mater. Mycol. Phytopath. Leningrad 5: 3 (1926) : Boeremia exigua var. linicola (Naumov & Vassilijevsky) Aveskamp, Gruyter & Verkley, in Aveskamp et al., Stud. Mycol. 65: 39 (2010) Reference Strain: CBS 116.76 (= reference specimen sensu Van der Aa et al. 1973; Boerema et al. 2004; Aveskamp et al. 2010; Chen et al. 2015). The strains CBS 109.49, CBS 114.28 and CBS 248.38 clustered together with the representative strain CBS 116.76 of B. exigua var. linicola assigned by Van der Aa et al. (1973) in our phylogenetic analyses (Fig. 2). The multigene loci sequence data for these four strains are almost identical. Here we elevate B. exigua var. linicola to B. linicola and assign CBS 116.76 as the reference specimen for this species. Boeremia opuli (Qian Chen, Crous & L. Cai) Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555809 : Boeremia exigua var. opuli Qian Chen, Crous & L. Cai, in Chen et al., Stud. Mycol. 87: 128 (2017) 51 Holotype: USA, from seedlings of Viburmum opulus (Caprifoliaceae), 2014, W.J Duan, HMAS 247147, ex-type culture CGMCC 3.18354. For a complete description see Chen et al. (2017). Chen et al. (2017) introduced this variety based on multigene analyses and morphological characters. Herein we elevate this taxon to species level as B. opuli. Morphologically this species can be distinguished based on larger pycnidia (Chen et al. 2017). It is phylogenetically closely related to B. exigua and B. gilvescens (Fig. 2) and differs in nine positions and eight positions in the RPB2 locus respectively. Boeremia populi (Gruyter & P. Scheer) Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555810 : Phoma exigua var. populi Gruyter & P. Scheer, J. Phytopath. 146(8–9): 413 (1998) : Boeremia exigua var. populi (Gruyter & P. Scheer) Aveskamp, Gruyter & Verkley, in Aveskamp et al., Stud. Mycol. 65: 39 (2010) Holotype: The Netherlands, Deil, from a twig of Populus (9) euramericana cv. Robusta (Salicaceae), Feb 1993, A.J.P. Oort, L 995.263.325, ex-type culture CBS 100167. For a complete description see de Gruyter et al. (2002). Boeremia exigua var. populi is known from Populus and Salix sp. (Aveskamp et al. 2010). Herein we elevate this variety to species level and introduce B. populi. In the phylogenetic analyses of Chen et al. (2015) (based on four gene regions) and in this paper (based on five gene regions), the type strain clusters with B. heteromorpha and we were unable to identify any base pair differences among these two species. Following Chen et al. (2015) and based on the host association of these two species and until further collections are done, herein we maintain B. populi as a distinct species from B. heteromorpha. Boeremia pseudolilacis (Aveskamp, Gruyter & Verkley), Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555811 : Boeremia exigua var. pseudolilacis Aveskamp, Gruyter & Verkley, in Aveskamp et al., Stud. Mycol. 65: 39 (2010) Holotype: The Netherlands, near Boskoop, from Syringa vulgaris (Oleaceae), 1994, J. de Gruyter, CBS H-20371, ex-type culture CBS 101207. For a complete description see Aveskamp et al. (2010). Boeremia exigua var. pseudolilacis was introduced by Aveskamp et al. (2010), based on morphological and phylogenetic support. Herein we raise the status to B. pseudolilacis to accommodate this taxon. This species can be identified from other Boeremia species on the basis of DAF and AFLP analyses (Aveskamp et al. 2009, 2010). 123 Author's personal copy 52 Boeremia rhapontica (Berner, Woudenb. & Tunali) Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555808 : Boeremia exigua var. rhapontica Berner, Woudenb. & Tunali, in Berner et al., Biological Control 81: 70 (2014) Holotype: Turkey, from Rhaponticum repens (Asteraceae), 2002, D. Berner, BPI 843350; ex-type culture CBS 113651. For a complete description see Berner et al. (2015). Boeremia exigua var. rhapontica was introduced by Berner et al. (2015) to accommodate the pathogen on Rhaponticum repens. Herein we elevate this to the species level and introduce B. rhapontica (for phylogenetic differences please see notes under B. coffeae). Recommended genetic markers (Genus level) –LSU and ITS Recommended genetic markers (Species level)—RPB2, TUB2, TEF1-a Accepted number of species: Twenty two species References: Boerema et al. (2004) (morphology and pathogenicity), Aveskamp et al. (2010), Chen et al. (2015, 2017), Jayasiri et al. (2017) (morphology and phylogeny), Berner et al. (2015) (morphology, pathogenicity and phylogeny). Calonectria De Not., Comm. Soc. Crittog. Ital. 2(fasc.3): 477 (1867) For synonyms see Index Fungorum (2019) Background Calonectria was first introduced based on Ca. daldiniana in 1867. Calonectria species are pathogenic to a wide range of woody and herbaceous plant hosts in tropical and subtropical areas (Crous 2002; Lechat et al. 2010; Lombard et al. 2010a, b; Chen et al. 2011; Li et al. 2017). The sexual morphs of Calonectria are characterised by yellow to dark red ascomata, with scaly to warty walls, and clavate, 4–8spored asci. They produce Cylindrocladium asexual morphs with branched conidiophores, cylindrical, septate conidia, and stipe extensions with terminal vesicles (Crous 2002; Lombard et al. 2010b, 2016; Li et al. 2017). Classification—Sordariomycetes, Hypocreaomycetidae, Hypocreales, Nectriaceae Type species—Calonectria pyrochroa (Desm.) Sacc., Michelia 1(no. 3): 308 (1878) Distribution — Worldwide Disease Symptoms—Box blight, Cutting rot, Damping off, Canker, Leaf spots, leaf and shoot blights, Red crown rot, Root rot Species of Calonectria are capable of causing diseases in all plant parts. Most diseases have been recorded from young plants or recent field plantings. Symptoms vary according to host species, host age or developmental stage, 123 Fungal Diversity (2019) 94:41–129 environmental conditions and the Calonectria species itself (Barnes and Linderman 2001). Leaf spots (caused by Ca.colhounii, Ca. ilicola, Ca. indusiata and Ca. pteridis) first appear as water-soaked lesions turning tan to dark brown, circular or irregular in shape surrounded by a red, dark brown or purple border with a chlorotic zone. Root necrosis is the main symptom of root rot caused by species such as Ca. crotalariae and Ca. ilicola (Lombard et al. 2010a). On conifers, there is necrosis of lateral and primary roots accompanied with blacking and splitting of the root cortex while on hardwoods, there is blackening of the root cortex with longitudinal cracking (Cordell and Skilling 1975). Lesions may coalesce and completely destroy the root. Crown infection can occur with the spread of root infection leading to stunting, discoloration of foliage, defoliation and plant death (Lombard et al. 2010a, 2011). Hosts—Calonectria species are soil borne pathogens and are mainly associated with forestry, agricultural and horticultural plants, on more than 100 plant families (Chen et al. 2011; Crous et al. 1991; Crous 2002, Gehesquiére et al. 2016; Lombard et al. 2010a, b; Li et al. 2017; Lopes et al. 2018). Calonectria species are less commonly associated with fruit rot as compared to leaf spot and root rot (Lopes et al. 2018). Morphological based identification and diversity Calonectria species were known by Cylindrocladium names for many years. Cylindrocladium species were commonly found in nature and well known plant pathogens. Later Calonectria was conserved (Hawksworth 2011; McNeill et al. 2012) over Cylindrocladium by Rossman et al. (2013). Most isolates were identified based on morphology. Later, polyphasic approaches based on morphology and sexual compatibility was used to delimit cryptic species (Schoch et al. 2001; Lombard et al. 2010a, b, 2016) and these studies have revealed that there are many species of Calonectria yet to be discovered (Lombard et al. 2016). Calonectria has been subjected to numerous taxonomic studies and 129 species have been recognized based on both morphological and molecular approaches (Crous and Wingfield 1994; Crous 2002; Lechat et al. 2010; Li et al. 2017; Lombard et al. 2010a, b, 2016; Maharachchikumbura et al. 2015, 2016; Lopes et al. 2018). Macroconidial dimensions and septation, and shape of the vesicle are the best diagnostic characters for identification of Calonectria (Schoch et al. 2000; Crous 2002; Li et al. 2017). Perithecial colour, ascospore number within the asci, and ascospore septation and dimensions are also important for sexual morph identification (Lombard et al. 2010a). However, perithecia of Calonectria species are morphologically very similar, hence are not useful in identification (Crous and Wingfield 1994; Crous 2002). However, intraspecific variation in vesicle shape and Author's personal copy Fungal Diversity (2019) 94:41–129 conidial dimensions are commonly used in identification of Calonectria, which can result in taxonomic confusion (Crous et al. 1998; Lombard et al. 2010b). Molecular based identification and diversity Morphological data are essential to supplement DNA sequence data for accurate species identification (Lombard et al. 2016). Earlier studies used ITS gene alone to separate Cylindrocladium species, however the ITS region contains few informative characters (Crous et al. 1999; Schoch et al. 2001; Lombard et al. 2010b). A genus-wide phylogeny can be inferred using TUB, TEF1-a, cmdA and His3 (Lombard et al. 2016; Crous 2002). The LSU gene also provides little information in resolving species of the genus (Lombard et al. 2010b). This study reconstructs the phylogeny of Calonectria based on analyses of a combined TEF1-a, TUB, cmdA and His3 sequence data (Table 3, Fig. 3). After Lombard et al. (2010a), this is the first multigene analysis for all the available Calonectria species. Calonectria species formed two major clades in our phylogenetic analysis, which define morphologically similar groups. Similar results were obtained in previous study by Lombard et al. (2010b) employing seven gene regions (including additional LSU, ITS and ACT sequence data). However, insufficient data are available for the His3 gene region in GenBank. Therefore, it is difficult to have comparative phylogenetic analyses (Table 3). Recommended genetic markers (Genus level)—LSU and ITS Recommended genetic markers (Species level)—TUB, TEF1-a, cmdA, His3, ACT Accepted number of species: There are 399 species epithets in Index Fungorum (2019) under this genus. However, 283 are accepted. References: Lombard et al. (2010a, b, c, d, 2016), Maharachchikumbura et al. (2015, 2016) (morphology and phylogeny) Coniella Höhn., Ber. dt. bot. Ges. 36(7): 316 (1918) = Pilidiella Petr. & Syd., Beih. Reprium nov. Spec. Regni veg. 42(1): 462 (1927) [1926]; = Schizoparme Shear, Mycologia 15(3): 120 (1923) For more synonyms see Index Fungorum (2019) Background Coniella Höhn. is a cosmopolitan genus which was introduced by von Höhnel (1918) and is typified by Coniella pulchella Höhn. (= Coniella fragariae (Oudem.) B. Sutton). Many Coniella species are known as plant pathogens causing foliar, fruit, leaf, stem and root diseases on a wide range of hosts, including some economically important hosts and have gained considerable attention from the phytopathological community (van Niekerk et al. 53 2004; Alvarez et al. 2016; Chethana et al. 2017). Several species in this genus have a saprobic lifestyle, occurring in leaf litter, rotting bark and in soil (Alvarez et al. 2016). Several species also occur as endophytes (Alvarez et al. 2016), parasites on unrelated hosts (C. straminea Samuels et al. 1993), and as secondary invaders of plants tissues infected by other organisms or injured by other causes (Ferreira et al. 1997). Classification– Sordariomycetes, Sordariomycetidae, Diaporthales, Schizoparmaceae Type species—Coniella fragariae (Oudem.) B. Sutton, Mycol. Pap. 141: 47 (1977) Distribution—Worldwide Disease Symptoms—foliar, fruit, stem and root lesions, white rot, crown rot. On leaves lesions are marginal, irregular with various shaded brown centres. Light brown specks gradually become reddish-brown larger specks causing wilting and dieback. Fruits may shrivel and change colour to brown. Diseases on major economic hosts including white rot on grapes (Coniella diplodiella and Coniella vitis; Chethana et al. 2017), fruit and leaf diseases of strawberry (C. castaneicola; Mass 1998), cankers, crown rots, die backs, fruit rots, leaf spots, shoot blights, and twig blights on pomegranates (C. granati; Mirabolfathy et al. 2012; Chen et al. 2014). Hosts—Wide variety of hosts belonging to Combretaceae, Malvaseae, Myrtaceae, Rosaceae and Vitaceae. Some Coniella species exhibit high host specificity (C. destruens and C. eucalyptorum on Eucalyptus, C. quercicola on Quercus sp., C. crousii on Terminalia sp., C. diplodiella and C. diplodiopsis on Vitis sp., and C. tibouchinae on Tibouchina sp.; Alvarez et al. 2016). Morphological based identification and diversity Coniella has been subjected to comprehensive morphomolecular studies and has undergone several taxonomic refinements over the years (Sutton 1980; Nag Raj 1993; Rossman et al. 2007; van Niekerk et al. 2004; Alvarez et al. 2016). Sutton (1980) and Nag Raj (1993) regarded Pilidiella as a synonym of Coniella based on conidial morphology. Samuels et al. (1993) stated Schizoparme as the sexual morph and positioned it in Melanconidaceae. Later, Castlebury et al. (2002) named Pilidiella and Coniella as Schizoparme complex and showed their distinct lineage in Diaporthales. Following Castlebury et al. (2002) and Rossman et al. (2007) established a new family, Schizoparmaceae, including the above three genera viz. Coniella, Pilidiella and Schizoparme. Maharachchikumbura et al. (2015, 2016) and Wijayawardene et al. (2016, 2018) accepted Schizoparmaceae as a well established family comprising Coniella, Pilidiella and Schizoparme. Alvarez et al. (2016) showed that Coniella, 123 Author's personal copy 54 Fungal Diversity (2019) 94:41–129 Table 3 Calonectria. Details of the isolates used in the phylogenetic tree Species Isolate TEF1-a His3 cmdA TUB Calonectria acicola CBS 114812* GQ267291 DQ190692 GQ267359 DQ190590 Ca. aciculata CMW 47645*; CERC 5342; CBS 142883 MF442644 MF442759 MF442874 MF442989 – 5342; CBS 142883 Ca. aconidialis CBS 136086* KJ462785 KJ463133 KJ463017 Ca. amazonica CBS 116250*; CPC 3534 KX784682 – KX784555 KX784612 Ca. amazoniensis CBS 115440*; CPC 3885 KX784685 – KX784558 KX784615 Ca. angustata CBS 109065*; CPC 2347; CBS 114544 FJ918551 DQ190696 GQ267361 AF207543 Ca. arbusta CBS 136079*; CMW 31370; CERC1705 KJ462787 KJ463135 KJ463018 – Ca. asiatica CBS 114073*; CMW 23782; CBS 112954 AY725705 AY725658 AY725741 AY725616 DQ190596 SFE 726; CPC Ca. australiensis 3900 CBS 112954* GQ267293 DQ190699 GQ267363 Ca. avesiculata CBS 313.92*; CMW 23670; CPC 2373; ATCC 38226 GQ267294 – GQ267364 – Ca. blephiliae CBS136425*; CPC21859 KF777243 – – KF777246 FJ696388 Ca. brachiatica CBS 123700*; CMW 25298 GQ267296 FJ696396 GQ267366 Ca. brasiliensis CBS 230.51*; CMW 23670; CPC 2390 GQ267328 GQ267259 GQ267421 GQ267241 Ca. brassiana CBS 134855*; CBS 13485 KM395883 – KM396057 KM395970 Ca. brassicae CBS 111869*; CMW 30982; CPC 2409; PC 551197 FJ918566 DQ190720 GQ267382 AF232857 Ca. brassicicola CBS 112841*; CPC 4552 KX784689 – KX784561 KX784619 Ca. brevistipitata CBS 115671*; CPC 94 KX784693 – KX784565 KX784623 Ca. canadiana CBS 110817*; CPC 499 GQ267297 – AY725743 AF348212 Ca. candelabrum CPC 1675 FJ972525 – GQ267367 FJ972426 Ca. cerciana CBS 123693*; CMW 25309 FJ918559 FJ918528 GQ267369 FJ918510 Ca. chinensis CBS 114827*; CMW 23674; CPC 4101 AY725710 AY725661 AY725747 AY725619 Ca. citri CBS 186.36*; CMW 23675 GQ267299 GQ267371 GQ267247 AF333393 Ca. clavata CBS 114557*; ATCC 66389; CPC 2536 GQ267305 DQ190623 GQ267377 AF333396 Ca. cliffordiicola Ca. colhounii CBS 111812*; CPC 2631 CBS 293.79*; CMW 30999 KX784694 GQ267301 – DQ190639 KX784566 GQ267373 KX784624 DQ190564 Ca. colombiana CBS 115127*; CMW 30871; CPC 1160 FJ972492 FJ972442 GQ267455 FJ972423 Ca. colombiensis CBS 112220*; CMW 23676; CPC 723 AY725711 AY725662 AY725748 GQ267207 Ca. crousiana CBS 127198*; CMW 27249 HQ285822 – – HQ285794 Ca. curvispora CBS 116159*; CMW 23693 GQ267302 AY725664 GQ267374 AF333394 Ca. cylindrospora CBS 110666; CPC 496 FJ918557 FJ918527 GQ267423 FJ918509 Ca. densa CBS 125261*; CMW 31182 GQ267352 – GQ267444 GQ267232 Ca. duoramosa CBS 134656*; LPF434 KM395853 KM396110 KM396027 KM395940 Ca. ecuadorensis CBS 111706* KX784747 – KX784604 KX784674 Ca. ecuadoriae CBS 111406*; CPC 1635 GQ267303 DQ190705 GQ267375 DQ190600 Ca. ericae CBS 114458*; CPC 2019 KX784699 – KX784571 KX784629 Ca. eucalypti CBS 125275* GQ267338 GQ267267 GQ267430 GQ267218 Ca. eucalypticola CBS 134847* KM395877 – KM396051 KM395964 Ca. expansa CBS 136247*; CMW 31392; CERC 1727 KJ462798 KJ463146 KJ463029 KJ462914 Ca. foliicola Ca. fujianensis CBS 136641*; CMW 31393; CERC 1728 CBS 127201*; CMW 27257 KJ462800 HQ285820 – HQ285806 KJ463031 – KJ462916 HQ285792 Ca. glaebicola CBS 134852* KM395879 KM396136 KM396053 KM395966 Ca. gordoniae CBS 112142*; CPC 3136; ATCC 201837 GQ267309 DQ190708 GQ267381 AF449449 Ca. gracilipes CBS 111141* GQ267311 DQ190644 GQ267385 DQ190566 Ca. gracilis CBS 111807* GQ267323 DQ190646 GQ267407 AF232858 Ca. guangxiensis CBS 136092*; CMW 35409; CERC 1900; CPC 23506 KJ462803 KJ463151 KJ463034 KJ462919 123 Author's personal copy Fungal Diversity (2019) 94:41–129 55 Table 3 (continued) Species Isolate TEF1-a His3 cmdA TUB Ca. hainanensis CBS 136248*; CMW 35187; CERC 1863 KJ462805 KJ463152 KJ463036 – Ca. hawksworthii CBS 111870*; CPC 2405; MUCL 30866 FJ918558 DQ190649 GQ267386 AF333407 Ca. henricotiae CBS 138102*; CB045 – KF815185 KF815157 JX535308 KC491228 Ca. hodgesii CBS 133609*; LPF 245 KC491225 – KC491222 Ca. honghensis CMW 476695*; CERC 5572; CBS 142885 MF442665 MF442780 MF442895 MF442997 Ca. hongkongensis CBS 114828*; CPC 4670 AY725717 AY725667 AY725755 AY725622 Ca. humicola CBS 125251* GQ267353 GQ267282 GQ267445 GQ267233 Ca. hurae Ca. ilicicola CBS 114551, CMW 16720; CPC 2344 CBS 190.50*; CMW 30998; IMI 299389 FJ918548 AY725726 DQ190728 AY725676 GQ267387 AY725764 AF333408 AY725631 Ca. indonesiae CBS 112823*; CMW 23683; CPC 4508 AY725718 AY725668 AY725756 AY725623 Ca. indonesiana CBS 112936* KX784701 – KX784573 KX784631 Ca. indusiata CBS 144.36* GQ267332 DQ190653 GQ267453 GQ267239 Ca. insularis CBS 114558*; CPC 768 FJ918556 – GQ267389 AF210861 Ca. kyotensis CBS 114525* AY725713 – AY725750 AF348215 Ca. lageniformis CBS 111324*; CPC 1473 KX784702 – KX784574 KX784632 Ca. lantauensis CMW 47252*; CERC 3302; CBS 142888 MF442677 MF442792 MF442907 – Ca. lateralis CBS 136629*; CMW 31412; CERC 1747 KJ462840 KJ463186 KJ463070 KJ462955 Ca. lauri CBS 749.70* GQ267312 GQ267250 GQ267388 GQ267210 Ca. leguminum CBS 728.68* FJ918547 DQ190654 GQ267391 AF389837 Ca. leucothoes CBS 109166*; CPC 2385; ATCC 64824 FJ918553 FJ918523 GQ267392 FJ918508 Ca. lichi CERC 8866* MF527039 MF527055 MF527071 MF527097 Ca. longiramosa CBS 116319* KX784705 – KX784577 KX784635 Ca. machaerinae Ca. macroconidialis CBS 123183*; CPC 15378 CBS 114880*; CPC 307 KX784706 GQ267313 – – – GQ267393 KX784636 – Ca. madagascariensis CBS 114572*; CPC 2252 GQ267314 DQ190658 GQ267394 DQ190572 Ca. magnispora CBS 136249*; CMW 35184; CERC 1860 KJ462841 KJ463187 KJ463071 KJ462956 Ca. malesiana CBS 112752*; CPC 4223 AY725722 AY725672 AY725760 AY725627 Ca. maranhensis CBS 134811* KM395861 KM396118 KM396035 KM395948 Ca. metrosideri CBS 133603* KC294310 KC294308 KC294304 KC294313 Ca. mexicana CBS 110918* FJ972526 FJ972460 GQ267396 AF210863 Ca. microconidialis CBS 136638*; CMW 31487; CERC 1822 KJ462845 KJ463191 KJ463075 KJ462960 Ca. montana CERC 8952* MF527049 MF527065 MF527081 MF527107 KT964769 Ca. monticola CBS 140645*; CPC 28835 KT964773 – KT964771 Ca. morganii CBS 119670; CPC 12766; DISTEF-GP1 GQ421797 DQ521602 – DQ521600 Ca. mossambicensis CMW 36327* JX570718 JX570726 JX570722 – Ca. multilateralis CBS 110932*; CPC 957 KX784712 – KX784580 KX784642 Ca. multinaviculata CBS 134858*; LPF233 KM395898 KM396155 KM396072 KM395985 Ca. multiphialidica CBS 112678* AY725723 AY725673 AY725761 AY725628 Ca. multiseptata Ca. naviculata CBS 112682* CBS 101121 FJ918535 GQ267317 DQ190659 GQ267252 GQ267397 GQ267399 DQ190573 GQ267211 Ca. nemoralis CBS 116249* KX784752 – KX784609 KX784679 Ca. nemoricola CBS 134837* KM395892 KM396149 KM396066 KM395979 Ca. nymphaeae CBS 131802*; HGUP 100003 KC555273 – – JN984864 Ca. octoramosa CBS 111423* KX784746 – KX784603 KX784673 Ca. orientalis CBS 125260* GQ267356 GQ267285 GQ267448 GQ267236 Ca. ovata CBS 111299* GQ267318 GQ267253 GQ267400 GQ267212 Ca. pacifica CBS 109063*; CMW 16726; IMI 354528 AY725724 GQ267255 AY725762 GQ267213 Ca. papillata CBS 136097*; CMW 37976; CERC 1939 KJ462849 KJ463195 KJ463079 KJ462964 123 Author's personal copy 56 Fungal Diversity (2019) 94:41–129 Table 3 (continued) Species Isolate TEF1-a His3 cmdA TUB Ca. paracolhounii CBS 14679*; CPC 2445 KX784714 – KX784582 KX784644 Ca. paraensis CBS 134669*; LPF430 KM395837 KM396094 KM396011 KM395924 Ca. parakyotensis CBS 136085*; CMW 35169; CERC 1845 KJ462851 KJ463197 KJ463081 – Ca. parva CBS 110798*; CPC 410 KX784716 – KX784583 KX784646 Ca. parvispora CBS 111465* KX784717 – KX784584 DQ190607 Ca. pauciramosa CMW 5683*; CPC 971 FJ918565 FJ918531 GQ267405 FJ918514 Ca. penicilloides CBS 174.55*; IMI 299375 GQ267322 GQ267257 GQ267406 AF333414 Ca. pentaseptata Ca. piauiensis CBS 136087*; CMW 35177; CERC 1853 CBS 134850* KJ462853 KM395886 KJ463199 KM396143 KJ463083 KM396060 KJ462966 KM395973 Ca. pini CBS 123698* GQ267344 – GQ267436 GQ267224 Ca. plurilateralis CBS 111401*; CPC 1637 KX784719 – KX784586 KX784648 Ca. pluriramosa CBS 136976*; CMW 31440; CERC 1774 KJ462882 KJ463228 KJ463112 KJ462995 Ca. polizzii CBS 123402* FJ972488 FJ972438 – FJ972419 Ca. propaginicola CBS 134815*; LPF220 KM395866 KM396129 KM396040 KM395953 Ca. pseudobrassicae CBS 134662*; LPF280 KM395849 KM396106 KM396023 KM395936 Ca. pseudocerciana CBS 134824* KM395875 KM396132 KM396049 KM395962 Ca. pseudocolhounii CBS 127195*; CMW 27209 HQ285816 HQ285802 – HQ285788 Ca. pseudoecuadoriae CBS 111402*; CPC 1639 KX784723 – KX784589 KX784652 Ca. pseudohodgesii CBS 134818* KM395817 – KM395991 KM395905 Ca. pseudokyotensis CBS 137332*; CMW 31439; CERC 1774 KJ462881 KJ463227 KJ463111 KJ462994 Ca. pseudometrosideri CBS 134845* KM395821 – KM395995 KM395909 Ca. pseudomexicana CBS 130354*; DISTEF-TCROU1 JN607296 JN607266 – JN607281 Ca. pseudonaviculata Ca. pseudopteridis CBS 114417*; CPC 10926 CBS 163.28*; IMI 299579 a GQ267325 KM395902 – – GQ267409 KM396076 GQ267214 – Ca. pseudoreteaudii CBS 123694*; CMW 25310 FJ918541 FJ918519 GQ267411 FJ918504 Ca. pseudoscoparia CBS 125257* GQ267349 GQ267278 GQ267441 GQ267229 Ca. pseudospathiphylli CBS 109165*; CPC 1623 FJ918562 AF348241 GQ267412 FJ918513 Ca. pseudospathulata CBS 134841* KM395896 KM396153 KM396070 KM395983 Ca. pseudoturangicola CMW 474965*; CERC 7126; CBS 142890 MF442750 MF442865 MF442980 MF443080 Ca. pseudouxmalensis CBS 110924*; CPC 942 KX784726 – – KX784654 Ca. pseudovata CBS 134675*; LPF285 KM395859 KM396116 KM396033 KM395946 Ca. pseudoyunnanensis CMW 476555*; CERC 5376; CBS 142892 MF442753 MF442868 MF442983 MF443083 Ca. pteridis CBS 111793*; ATCC 34395; CPC 2372 FJ918563 DQ190679 GQ267413 DQ190578 Ca. putriramosa CBS 111449*; CPC 1951 KX784728 – KX784591 KX784656 Ca. queenslandica CBS 112146*; CPC 3213 FJ918543 FJ918521 GQ267415 AF389835 KM395942 Ca. quinqueramosa CBS 134654*; LPF065 KM395855 KM396112 KM396029 Ca. reteaudii CBS 112144*; CMW 30984; CPC 3201 FJ918537 DQ190661 GQ267417 AF389833 Ca. robigophila CBS 134652* KM395850 KM396107 KM396024 KM395937 Ca. rumohrae Ca. seminaria CBS 111431*; CPC 1716 CBS 136632*; CMW 31450; CERC 1785; CPC 23488 FJ918549 KJ462885 DQ190675 KJ463231 GQ267419 KJ463115 AF232871 KJ462998 Ca. silvicola CBS 135237* KM395891 – KM396065 KM395978 Ca. spathiphylli CBS 114540; ATCC 44730; CPC 2378 GQ267330 – GQ267424 AF348214 Ca. spathulata CBS 555.92* GQ267331 GQ267261 GQ267427 GQ267215 Ca. sphaeropedunculata CBS 136081*; CMW 31390; CERC 1725 KJ462890 KJ463236 KJ463120 KJ463003 Ca. stipitata CBS 112513*; CPC 3851 KX784734 – KX784596 KX784661 Ca. sulawesiensis CBS 125277* GQ267342 – GQ267434 GQ267222 Ca. sumatrensis CBS 112829*; CMW 23698; CPC 4518 AY725733 AY725696 AY725771 AY725649 Ca. syzygiicola CBS 112831*; CPC 4511 KX784736 – – KX784663 123 Author's personal copy Fungal Diversity (2019) 94:41–129 57 Table 3 (continued) Species Isolate TEF1-a His3 cmdA TUB KM395930 Ca. telluricola CBS 134664*; LPF217 KM395843 KM396100 KM396017 Ca. tereticornis CBS 111301*; CPC 1429 KX784737 – – KX784664 Ca. terrae-reginae CBS 112151*; CPC 3202 FJ918545 FJ918522 GQ267451 FJ918506 Ca. terrestris CBS 136642*; CMW 35180; CERC 1856 KJ462891 KJ463237 KJ463121 KJ463004 Ca. terricola CBS 116247*; CPC 3583 KX784738 – – KX784665 Ca. tetraramosa CBS 136635*; CMW 31474*; CERC 1809*; CPC 23489 KJ462898 KJ463244 KJ463128 KJ463011 Ca. trifurcata CBS 112753* KX784740 – KX784598 KX784667 Ca. tropicalis Ca. tucuruiensis CBS 116271; CPC 3559 CBS 114755* KX784742 KX784743 – – KX784599 KX784600 KX784669 KX784670 Ca. tunisiana CBS 130357* JN607291 JN607261 – JN607276 Ca. turangicola CBS 136077*; CMW 31411; CERC 1746; CPC23479 KJ462900 KJ463246 – KJ463013 Ca. uniseptata CBS 413.67* GQ267307 GQ267248 GQ267379 GQ267208 Ca. uxmalensis CBS 110925*; CPC 945 KX784708 – – KX784638 Ca. variabilis CBS 112691; CPC 2506 GQ267335 GQ267264 GQ267458 GQ267240 Ca. venezuelana CBS 111052*; CPC 1183 KX784744 – KX784601 KX784671 Ca. vietnamensis CBS 112152* KX784745 – KX784602 KX784672 Ca. yunnanensis CMW 476445*; CERC 5339; CBS 14289 MF442758 MF442873 MF442988 MF443088 Ca. zuluensis CBS 125268; CMW 9188 FJ972483 FJ972433 GQ267459 FJ972414 Curvicladiella cignea CBS 109167*; CPC 1595; MUCL 40269 KM231867 KM231461 KM231287 KM232002 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher stains are in bold Pilidiella and Schizoparme formed a monophyletic clade in Schizoparmaceae, and proposed to adopt Coniella (the older asexual typified name) over Pilidiella and Schizoparme agreeing with Art. 59.1 of the International code of nomenclature for algae, fungi and plants. Based on conidial pigmentation, van der Aa (in von Arx 1973) and von Arx (1981) treated Coniella and Pilidiella as separate genera, Coniella having dark brown conidia and Pilidiella having hyaline conidia. However, Sutton (1980) and Nag Raj (1993) rejected conidial pigmentation as a distinguishing character and synonymized Pilidiella under the older name, Coniella. Since the introduction of molecular data in species delimitation, many studies have demonstrated that these two asexual genera should be distinct (Castlebury et al. 2002; van Niekerk et al. 2004; Wijayawardene et al. 2016). Due to the many species complexes and similar morphological characters, Alvarez et al. (2016) stated that new species of Coniella must be identified based on both DNA sequence data and morphological characters. Following Alvarez et al. (2016) and Chethana et al. (2017) adapted a morphological approach in conjunction with multi-gene phylogeny and Genealogical Concordance Phylogenetic Species Recognition (GCPSR) approach in defining species boundaries. Colony and conidial morphology are the primary characters to identify species within this genus (Ellis 1971, 1976; Simmons 1992). In terms of morphological characters, Coniella species share several characteristics including conidiomatal anatomy, conidiophores and conidiogenesis. However, morphological characters such as conidial colour, shape, size, presence of basal or lateral mucoid appendages, germ slits, guttules, and cultural characteristics differ depending on the species. Molecular based identification and diversity Although Coniella has received much attention, few phylogenetic studies have been conducted. Castlebury et al. (2002) first determined phylogeny of Coniella in Diaporthales using the large subunit (LSU) nuclear ribosomal DNA (nrDNA) sequence data. Following Castlebury et al. (2002), most studies have used single gene phylogeny in resolving Coniella. Van Niekerk et al. (2004) used four genes (LSU, ITS, TEF1-a and His3), whereas Miranda et al. (2012) used two genes (ITS and LSU) in their single gene phylogenies. Wijayawardene et al. (2016) combined the latter genes in their phylogenetic analysis. Confusion and inconsistencies revealed by Wijayawardene et al. (2016) leading to poor species delimitation in Coniella was addressed by Alvarez et al. (2016) using a multi-gene phylogenetic approach (ITS, LSU, RPB2 and TEF1-a). Chethana et al. (2017) resolved the taxonomy by combining multi-gene phylogenetic analysis together with GCPSR (ITS, LSU, His3 and TEF1-a). In this section, we reconstruct the phylogeny (Table 4, Fig. 4) of Coniella based on 123 Author's personal copy 58 a combined ITS, LSU, His3 and TEF1-a sequence data. Phylogeny generated herein depicts 34 well-supported clades corresponding to 34 species. The phylogenetic analysis is similar to that of Alvarez et al. (2016) and Chethana et al. (2017). However, the current study includes several new taxa which were introduced recently. Since this genus is of importance to plant pathology, a descriptive study of these species, especially their population dynamics, comparative and functional genomics, will contribute to understanding pathogenic potential and ecological roles of Coniella species infecting agricultural crops. Recommended genetic markers (Genus level)—LSU and ITS Recommended genetic markers (Species level)—ITS, LSU, TEF 1-a, RPB2 and His3 For the preliminary identification of Coniella species, LSU and ITS gene regions are recommended (Castlebury et al. 2002; van Niekerk et al. 2004; Wijayawardene et al. 2016). Combined analysis using ITS, LSU, TEF1-a, RPB2 and His3 (selection of 4 genes) should be used in resolving species, with recommended primers (Alvarez et al. 2016; Chethana et al. 2017). Accepted number of species: There are 60 species epithets in Index Fungorum (2019) under this genus. However, 34 are accepted. References: van Niekerk et al. (2004), Maharachchikumbura et al. (2015, 2016), Alvarez et al. (2016) (morphology and phylogeny), Chethana et al. (2017) (morphology, phylogeny and pathogenicity). Corticiaceae Herter, Krypt.-Fl, Brandenburg (Leipzig) 6(1):70 (1910) Background Corticiaceae is one of the oldest family names established by Heter (1910) and for a long time was a repository for all basidiomycetes sharing corticioid type of fruiting body, that is basidiomes with resupinate or cortex-like appearance formed over the surface of the substrata. In this traditional sense, Corticiaceae included many distantly related taxa, now shown to be distributed in different orders of basidiomycete phylogeny (Binder et al. 2005). The family name was conserved against Vuilleminiaceae by Pouzar (1985). Corticiaceae taxa are widespread and inhabit a wide range of substrata. Corticiaceae present diverse nutritional habits, with saprotrophic, plant pathogenic, mycoparasitic, lichenized and lichenicolous members. Species of Limonomyces and Waitea are plant pathogens, whereas Erythricium and Laetisaria also include saprotrophic, mycoparasitic, or lichenicolous species. Several species in this family form visible pink fruiting bodies on living or dead plants. The 123 Fungal Diversity (2019) 94:41–129 Fig. 3 Phylogenetic tree generated by maximum likelihood analysis c of combined TEF1-a, TUB, cmdA and His3 sequence data of Calonectria species. Related sequences were obtained from GenBank. One hundred sixty strains are included in the analyses, which comprise 1946 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 35122.522366 is presented. The matrix had 1231distinct alignment patterns, with 15.02% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.219321, C = 0.325516, G = 0.222910, T = 0.232253; substitution rates AC = 1.329187, AG = 3.755831, AT = 1.528969, CG = 0.930598, CT = 4.519462, GT = 1.000000; gamma distribution shape parameter a = 0.749195. Maximum likelihood bootstrap support (MLBT C 65%) and posterior probabilities (BIPP C 0.90) from Bayesian inference analysis are indicated respectively near the nodes. The ex-type strains are in bold and new isolates in blue. The scale bar indicates 0.06 nucleotide changes per site. Tree is rooted to Curvicladiella cignea phytopathogenic species are mostly the agent of ‘pink disease’ in turfgrasses or woody perennials. Several taxa in this family are known only as asexual morphs, while plant pathogenic genera are sexual morph-typified and form sexual fruiting bodies, in addition to their asexual state. Classification—Agaricomycetes, incertae sedis, Corticiales Type– Corticium Pers., Neues Mag. Bot. 1:110 (1794) Distribution—Worldwide Disease Symptoms—Brown ring patch, Pink disease, Pink Patch disease, Red thread Sheath spot. The symptoms include production of salmon pink mycelium on branches and stems of trees resulting in twig and branch injuries, stem canker and eventually death of the host (Sebastianes et al. 2007). With sheath spot disease, lesions first appear as water-soaked areas with grey-green to straw coloured centers and a brown margin. Leaves of infected sheaths usually turn yellow and die (Lanoiselet et al. 2007). Circular or irregular small patches of tan to yellow–brown are the initial symptoms of brown ring patch disease. The affected grasses eventually develop brownish rings (Toda et al. 2005). In pink patch and red thread disease, small water-soaked spots covering a larger portion of the grass leaf can be observed. The tissue dries out and fades to a tan colour and is covered with pink mycelium. Hosts—Citrus sp., Coffea sp., Hevea sp., Poaceae Morphological based identification and diversity The 10th edition of Dictionary of Fungi (Kirk et al. 2008), enumerates 29 genera and 136 species associated with Corticiaceae. This figure is however, outdated as many taxa recorded there do not belong to Corticiaceae, following the most recent phylogenies. The family was delimited in its strict sense by Ghobad-Nejhad et al. (2010). They found that Corticiaceae forms a small, well- Author's personal copy Fungal Diversity (2019) 94:41–129 59 123 Author's personal copy 60 Fungal Diversity (2019) 94:41–129 Fig. 3 continued supported clade in Corticiales containing several polyphyletic genera in need of revision, and confirmed that it is the most diverse family in Corticiales with regard to its high ecological and nutritional diversity (Lawrey et al. 2008). Corticiaceae currently encompasses about ten 123 genera and about 40 species. A taxonomic and phylogenetic revision of the family is underway (Ghobad-Nejhad et al., unpublished), which is out of the scope of this study. The four genera with plant pathogenic taxa viz., Laetisaria, Author's personal copy Fungal Diversity (2019) 94:41–129 Table 4 Coniella. Details of the isolates used in the phylogenetic analyses 61 Species Isolate ITS His3 LSU TEF 1-a C. africana CBS 114133* AY339344 AY339309 AY339293 AY339364 C. crousii NFCCI 2213 HQ264189 – – – C. diplodiella CBS 111858* AY339323 AY339297 AY339284 AY339355 C. diplodiopsis CBS 590. 84* AY339334 AY339308 AY339288 AY339359 C. duckerae CBS 142045* KY924929 – – – C. erumpens CBS 523.78* KX833533 – KX833361 KX833630 C. eucalyptigena CBS 139893* KR476725 – KR476760 – C. eucalyptorum CBS 112640* AY339338 – AY339290 KX833637 C. fragariae CBS 172.49* AY339317 – AY339282 AY339352 C. fusiformis CBS 141596* KX833576 – KX833397 KX833674 C. granati CBS 252.38 AY339342 – AY339291 AY339362 C. hibisci CBS 109757 KX833581 – – KX833689 C. javanica CBS 455.68* KX833583 – KX833403 KX833683 C. koreana CBS 143.97* KX833584 – AF408378 KX833684 C. lanneae C. limoniformis CBS 141597* CBS 111021* KX833585 AY339346 – AY339310 KX833404 KX833405 KX833685 KX833686 C. lustricola DAOMC 251731* MF631778 – MF631799 MF651899 C. macrospora CBS 524.73* AY339343 – AY339292 AY339363 C. malaysiana CBS 141598* KX833588 KX833406 KX833688 C. hibisci CBS 109757* KX833589 – AF408337 KX833689 C. nicotianae CBS 875.72* KX833590 – KX833407 KX833690 C. nigra CBS 165.60 * AY339319 – KX833408 KX833691 C. obovata CBS 111025 AY339313 – KX833409 KX833692 C. paracastaneicola CBS 141292* KX833591 – KX833410 KX833693 C. peruensis CBS 110394* KJ710463 – KJ710441 KX833695 C. pseudogranati CBS 137980* KJ869132 – KJ869189 – * C. pseudostraminea CBS 112624 KX833593 – KX833412 KX833696 C. quercicola CBS 904.69* KX833595 – KX833414 KX833698 C. solicola CBS 766.71* KX833597 – KX833416 KX833701 Coniella sp. CBS 114006 AY339347 AY339311 AY339295 KX833703 C. straminea C. tibouchinae CBS 149.22 CBS 131594* AY339348 JQ281774 AY339312 – AY339296 JQ281776 AY339366 JQ281778 C. vitis MFLUCC 16–1399* KX890008 KX890033 KX890083 KX890058 C. wangiensis CBS 132530* NR-111764 – NG-042686 KX833705 Melanconiella sp. CBS 110385 KX833599 – KX833420 KX833707 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher stains are in bold Limonomyces, Eryhtricium, and Waitea are discussed in the following parts. Tretopileus is briefly noted here. Tretopileus is a small asexual genus established by Dodge (1946) for a curious fungus found on cactus. The genus is typified by T. opuntiae, and two more species, T. indicus and T. sphaerophorus, were subsequently added to the genus. Okada et al. (1998) showed that T. sphaerophorus was placed in ‘‘Aphyllophorales’’, But later studies confirmed its position in Corticiales (Rungjindamai et al. 2008), and within Corticiaceae (Ghobad-Nejhad et al. 2010). To date, only T. sphaerophorus has been subject to phylogenetic studies, while the affinities of the generic type as well as T. indicus are yet to be examined. Okada et al. (1998) believe that Tretopileus species may be weakly parasitic on plants. Most Corticiaceae species form visible pink fruiting bodies on living or dead plants. Basidia are usually large with a swollen base, producing large ellipsoid basidiospores. However, as stated above, the boundaries between genera are perplexing due to overlapping characters. Molecular based identification and diversity During efforts to unravel Agaricomycetes phylogeny, the lineages belonging to Corticiaceae have been restricted 123 Author's personal copy 62 Fig. 4 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, LSU, Histone and TEF1-a sequence data of Coniella species. Related sequences were obtained from GenBank. Thirty four strains are included in the analyses, which comprise 2877 characters including gaps. Tree was rooted with Melanconiella sp. (CBS 110385). Tree topology of the ML analysis was similar to the ones generated from MP and BI (Figures not shown). The best scoring RAxML tree with a final likelihood value of - 14885.549943 is presented. The maximum parsimonious dataset consisted of constant characters 2116, 509 parsimony-informative and with 23.84% of undetermined characters or gaps. Estimated base frequencies were as 123 Fungal Diversity (2019) 94:41–129 follows; A = 0.249654, C = 0.245318, G = 0.256486, T = 0.248542; substitution rates AC = 0.977807, AG = 2.195640, AT = 1.226082, CG = 0.712360, CT = 4.190875, GT = 1.000000; gamma distribution shape parameter a = 0.137391. The parsimony analysis of the data matrix resulted in the maximum of two equally most parsimonious trees with a length of 2459 steps (CI = 0.525, RI = 0.571, RC = 0.300, HI = 0.475) in the first tree. RAxML and maximum parsimony bootstrap support values C 50% (BT) are shown respectively near the nodes. Bayesian posterior probabilities C 0.95 (PP) and indicated as thickened black branches. The scale bar indicates 0.1 changes per site. The ex-type strains are in bold Author's personal copy Fungal Diversity (2019) 94:41–129 63 Fig. 5 Phylogram generated from bayesian analysis based on combined ITS, nSSU, nLSU, and mtSSU sequence data of Corticiaceae. Bayesian posterior probabilities are indicated above the nodes. The sequences were obtained from GenBank. Thirty one isolates were included in the analyses, comprising 3797 characters including gaps. The tree obtained from Bayesian analyses with the average standard deviation of split frequency equal to 0.005882 is presented. Among these, 2585 characters were constant, and 550 characters were variable but parsimony uninformative. The analyses run for 30 million generations and 8 MCMCMC chains, with 5000 sample frequency. The ITS partition was analysed with GTR ? G model of nucleotide evolution, while the nSSU, nLSU, and mtSSU datasets were analysed using GTR ? I ? G model, as suggested by MrModeltest. The ex-type (ex-epitype) and voucher strains are in bold. The scale bar indicates 0.03 changes per site. The tree is rooted with Cytidia salicina to a small clade more commonly named as ‘corticioid clade’. This clade was formally established as Corticiales by Hibbett et al. (2007). Corticiales was subsequently shown to encompass three well-supported clades recognized by Ghobad-Nejhad et al. (2010) under three family names Corticiaceae, Punctulariaceae and Vuilleminiaceae. Circumscription of most of genera in Corticiaceae is problematic and synapomorphies for generic and specific delimitations in Corticiaceae are not yet resolved. The phylogenetic tree provided (Fig. 5) is based on a combined dataset of ITS, nSSU, nLSU, and mtSSU sequence data (Table 5). This phylogenetic tree is largely in accordance with earlier studies, and provides the most conclusive phylogeny of the family to date. References: Binder et al. (2005), Hibbett et al. (2007), Ghobad-Nejhad et al. (2010) (morphology and phylogeny). Toda et al. (2005), Sebastianes et al. (2007) (molecular phylogeny and pathogenicity) Recommended genetic markers (Genus level)—LSU, mtSSU Recommended genetic marker (Species level)—ITS Accepted genera: In this family ten genera have been accepted, all with DNA molecular data. Elsinoe Racib. [as ‘Elsinoë’], Parasit. Alg. Pilze Java’s (Jakarta) 1: 14 (1900) Background Elsinoe was introduced by Raciborski (1900) based on E. canavaliae (Hyde et al. 2013; Jayawardena et al. 2014). von Arx & Müller (1975) placed this genus in Myriangiaceae based on the nature of its pseudoascostromata and parasitic nature. Later, the genus was placed in family Elsinoaceae (Barr 1979; Kirk et al. 2001; Lumbsch and Huhndorf 2007, 2010; Hyde et al. 2013; Jayawardena et al. 2014; Wijayawardene et al. 2017b). Elsinoe is characterized by forming scab-like lesions with pseudoascostromata containing three to eight bitunicate asci in each locule (Jayawardena et al. 2014).The asexual morph is the acervular coelomycetous Sphaceloma de Bary (2017a). 123 Author's personal copy 64 Fungal Diversity (2019) 94:41–129 Table 5 Corticiaceae. Details of the isolates used in the phylogenetic analyses Species Isolate ITS nLSU nSSU mtSSU Corticium roseum MG43 GU590877 EF537893a – – Cytidia salicina mg49 GU590881 HM046921 – AF214458a Erythricium atropatanum MG58* GU590876 GU590880 – – E. laetum MG72 GU590875 GU590878 – – E. laetum MG73 GU590874 GU590879 – – E. salmonicolor BNR-KT-06 EU435008 AY672680a – – E. salmonicolor BNR-BRVT-05 EU435009 AY672678a – – E. salmonicolor Royal Delicious KF029722 KF029722 – – Galzinia incrustans HHB-12952-sp – AF518617 AF518578 AF518679 Giulia tenuis BCC13066 – EF589739 EF589732 – Laetisaria arvalis L. fuciformis CBS 131.82* NJ-2 Jackson EU622841a EU118639 EU622842 AY293192 EU622843 AY293139 HQ168390 AY293232 L. lichenicola CBS 128705* NR_121484 HQ168400 HQ168399 HQ168389 Limonomyces culmigenus ATCC 22523 EU622849 EU622848 EU622847 – L. roseipellis CBS 299.82 EU622846 EU622844 EU622845 HQ168396 L. roseipellis T-13-1 KC193592 KF824726a AY613915a a KF824721a Marchandiomyces aurantiacus CBS 718.97 AY583324 AY583330 DQ915460 M. aurantiacus CBS 128706 HQ168397 HQ168397 HQ168398 Marchandiomyces buckii ATCC MYA 2992 (JL244-03)* – DQ915472 DQ915462 HQ168392 M. corallinus ATCC MYA 3182 AY583327a AY583331a DQ915464 HQ168393 M. lignicola ATCC MYA 3674 FJ172272a AY583332a DQ915465 HQ168391 M. marsonii ATCC MYA 4210* EU622840 EU622839 EU622838 HQ168395 M. nothofagicola JL-261-04 DQ915474 DQ915474 DQ915466 HQ168394 M. quercinus FCUG1166 KP864659b HM046929a – – Marchandiomphalina foliacea Palice 4369 AY542865 AY542865 AY542865 – M. foliacea Palice 2509 AY542864 AY542864 AY542864 – Tretopileus sphaerophorus Vuilleminia comedens JCM10092 T-583 – HM046880a – AF518666 AB006005 AF518594 – AF518699 Waitea circinata AFTOL-ID 1129 DQ356414a AY885164 – FJ440234a – FJ440232a – FJ440221a W. circinata SK-OA-W3-I HM597147 AD001658 W. circinata X-54 KC176341 KC176341 a – HQ168388 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold a Sequences obtained from a different isolate b Newly generated sequence Jenkins (1932a, b) proposed a connection between Sphaceloma and Elsinoe. As the sexual morph is not common in nature, morphological based identification of Elsinoe species is difficult. The asexual morph Sphaceloma frequently occurs in nature, however, its morphological characters overlap making identification of the species difficult. Examination of specimens collected in the field is also problematic due to the lack of fertile structures. Isolation of Elsinoe species is also challenging due to their slow growth (Jenkins 1932a, b). In past, scab symptoms have been considered as a major character in recognizing the presence of fungi belonging to this genus, when sporulation is absent (Bitancourt and Jenkins 1949). Fan et al. (2017) suggested 123 that even if spores are absent, species can be named if they have the support of successful isolations, resulting in cultures having common characteristics of the genus. The colonies of this genus are slow growing, raised, cerebriform or corrugated, dark red, orange or brown. If cultures cannot be obtained they should be considered as doubtful species until fertile specimens or pure cultures are obtained (Fan et al. 2017). Many studies over the past decade have identified secondary metabolites of this genus (Hyde et al. 2013). Elsinochrome is a non-host selective, light-activated polyketide-derived toxin produced by Elsinoe species (Chung and Liao 2008). This is a red-pigmented secondary Author's personal copy Fungal Diversity (2019) 94:41–129 metabolite mainly produced by E. fawecettii (Yang and Chung 2010). Elsinopirini is a decalin polyketide isolated as a colourless oil from E. pyri (Surup et al. 2018). Production of these secondary metabolites can be used in chemotaxonomy. Classification—Dothideomycetes, Dothideomycetidae, Myriangiales, Elsinoaceae Type species—Elsinoe canavaliae Racib. [as ‘canavalliae’], Parasit. Alg. Pilze Java’s (Jakarta) 1: 14 (1900) Distribution—Worldwide Disease Symptoms—Scab, Anthracnose of grapevine Many species cause scab like blemishes (Jayawardena et al. 2014). They can affect leaves, stems and fruits affecting the appearance as well as reducing the yield. Infected organs of some hosts (Cassava) develop severe distortions (Guatimosim et al. 2015). Hosts—All members of this genus are specialized plant pathogens causing diseases on many economically important crops such as Citrus, Malus, Rubus and Vitis (Hyde et al. 2013; Jayawardena et al. 2014; Fan et al. 2017). The species appear to have a narrow host range, usually limited to a single host (Fan et al. 2017). However, a few species have a broad host range e.g., E. anacardii, E. leucospermi, E. piri and E. viola. Morphological based identification and diversity Kirk et al. (2008) estimated that there are 48 species of Elsinoe and 52 species of Sphaceloma. There are 190 species epithets under Elsinoe and 169 epithets under Sphaceloma in Index Fungorum (Index Fungorum 2019). Most Elsinoe species described to date need to be recollected and epitypified. Fan et al. (2017) designated 13 epitypes based on taxonomy and phylogenetic data. In accordance with the ‘‘One Fungus, one name’’ concept, the sexual name Elsinoe was protected over Sphaceloma. Therefore, many names in Sphaceloma should be transferred to the genus Elsinoe. Fan et al. (2017) relocated 26 Sphaceloma species to Elsinoe. In their study, eight new species were introduced, leading to a total of 75 Elsinoe species supported by morphology and molecular data. Colony and spore morphology are the primary characters to identify species of Elsinoe (Fan et al. 2017). Species have overlapping colony and spore characters making identification based on morphology difficult. Therefore, use of DNA sequence data is crucial in identifying these species. Molecular based identification and diversity The first molecular study on this genus was by Tan et al. (1996), who investigated the genetic differences among the citrus scab pathogens E. fawcettii and E. australis from South America and S. fawcettii var. scabiosa from Australia. The asexual morph and sexual morph relationship 65 was resolved by Cheewangkoon et al. (2009) by analysing rDNA sequence data. Few molecular studies have been carried out on this genus. Schoch et al. (2006) and Boehm et al. (2009) using rDNA data showed that the species of Elsinoe constitute a subclade among the species of Myriangiaceae. However, Schoch et al. (2006) used only four Elsinoe strains and one Myrangium strain. Swart et al. (2001), based on ITS sequence data, delineated six Elsinoe species associated with the scab disease of Proteaceae and proposed three new species. Similar studies (e.g., Summerbell et al. 2006; Everett et al. 2011) described species of this genus associated with other host plants. Everett et al. (2011) and Hyde et al. (2013) carried out higher level phylogenetic studies on Dothideomycetes, which included strains of Elsinoe. Jayawardena et al. (2014) using the available sequence data on ITS, LSU, SSU, RPB2 and TEF1-a in GenBank provided evidence that Elsinoaceae can be considered as a separate family within the order Myriangiales. At the time, 12 Elsinoe species were included in this analysis, but ex-type sequence data was available for only a few species. Most species are based on old specimens without sequence data (Jayawardena et al. 2014). Fan et al. (2017) used 119 isolates representing 67 host genera from 17 countries and analysed a combined multigene analysis (ITS, LSU RPB2 and TEF1-a) with 64 ex-type strains. However, Jayawardena et al. (2014) and Fan et al. (2017) were unable to include the generic type E. canavaliae due to a lack of DNA data. Even though there are several excellent studies on this genus associated with plant diseases, very few species have any available cultures or DNA data (Jenkins 1932a, b; Bitancourt and Jenkins 1936). Therefore, epitypification from fresh collections is required to provide a stable and a workable taxonomy for this genus. This study reconstructs the phylogeny of Elsinoe based on a combined ITS, LSU, RPB2 and TEF1-a sequence data (Table 6, Fig. 6), updated with recently introduced species and it corresponds with previous studies. Recommended genetic marker (Genus level)—ITS Recommended genetic markers (Species level)—RPB2, TEF-1-a Accepted number of species: There are more than 200 species epithets in Index Fungorum (2019) under this genus. However, 75 species have molecular data are treated as accepted. References: Hyde et al. (2013) (morphology, taxonomy), Jayawardena et al. (2014), Fan et al. (2017) (morphology, phylogeny), Chung and Liao (2008), Surup et al. (2018) (Phytotoxin). Entyloma de Bary, Bot. Ztg. 32(7): 101 (1874) For synonyms see Index Fungorum (2019) 123 Author's personal copy 66 Fungal Diversity (2019) 94:41–129 Table 6 Elsinoe. Details of the isolates used in the phylogenetic analyses Species Isolate ITS LSU RPB2 TEF1-a Elsinoe abutilonis CBS 510.50* KX887185 KX886949 KX887068 KX886831 E. ampelina CBS 208.25 KX887186 KX886950 KX887069 KX886832 E. anacardii CBS 470.62* KX887189 KX886953 KX887072 KX886835 E. annonae CBS 228.64 KX887190 KX886954 KX887073 KX886836 E. arachidis CBS 511.50* KX887191 KX886955 KX887074 KX886837 E. arrudai CBS 220.50* KX887194 KX886958 KX887077 KX886840 E. asclepiadea CPC 18544* = RWB1202 = CBS 141937 KX887195 KX886959 KX887078 KX886841 E. australis CBS 314.32* KX887198 KX886962 KX887081 KX886844 E. banksiicola CBS 113734* = CPC1508 = CPC 1510 KX887199 KX886963 KX887082 KX886845 E. barleriicola CBS 471.62* = ATCC 14658 KX887200 KX886964 KX887083 KX886846 E. bidentis E. brasiliensis CBS 512.50* CPC 18528 = RWB 1133 KX887201 KX887204 KX886965 N/A KX887084 KX887087 KX886847 KX886850 E. caleae CBS 221.50* KX887205 KX886968 KX887088 KX886851 E. centrolobii CBS 222.50* KX887206 KX886969 KX887089 KX886852 E. citricola * CPC 18535 = RWB 1175 KX887207 KX886970 KX887090 KX886853 E. coryli CBS 275.76* KX887209 KX886972 KX887092 KX886855 E. diospyri CBS 223.50* KX887210 KX886973 KX887093 KX886856 E. embeliae CBS 472.62* KX887211 KX886974 N/A KX886857 E. erythrinae CPC 18542* = RWB 1196 KX887214 KX886977 KX887096 KX886860 * KX886861 E. eucalypticola CBS 124765 = CPC 13318 KX887215 KX886978 KX887097 E. eucalyptorum CBS 120084* = CPC 13052 KX887216 KX886979 KX887098 KX886862 E. euphorbiae CBS 401.63* KX887217 KX886980 KX887099 KX886863 E. fagarae CBS 514.50* KX887218 KX886981 KX887100 KX886864 E. fawcettii CBS 139.25* KX887219 KX886982 KX887101 KX886865 E. fici CBS 515.50 KX887223 KX886986 KX887105 KX886869 E. fici-caricae CBS 473.62* = ATCC 14652 KX887224 KX886987 KX887106 KX886870 E. flacourtiae E. freyliniae CBS 474.62* = ATCC 14654 CBS 128204* = CPC 18335 KX887225 KX887226 KX886988 KX886989 KX887107 KX887108 KX886871 KX886872 E. genipae CBS 342.39* KX887227 KX886990 KX887109 KX886873 E. genipae-americanae CBS 516.50* KX887228 KX886991 KX887110 KX886874 E. glycines * CBS 389.64 KX887229 KX886992 KX887111 KX886875 E. hederae CBS 517.50* KX887231 KX886994 KX887113 KX886877 E. ichnocarpi CBS 475.62* = ATCC 14655 KX887232 KX886995 KX887114 KX886878 E. jasminae CBS 224.50* KX887233 KX886996 KX887115 KX886879 E. jasminicola CBS 212.63* KX887234 KX886997 N/A KX886880 E. krugii CPC 18531* = RWB 1151 KX887235 KX886998 KX887116 KX886881 E. lagoa-santensis CBS 518.50* KX887239 KX887002 KX887120 KX886885 E. ledi CBS 167.33* KX887240 KX887003 KX887121 KX886886 E. lepagei CBS 225.50* KX887241 KX887004 KX887122 N/A E. leucospermi CBS 111207* = CPC 1380 KX887242 KX887005 KX887123 KX886887 E. lippiae * CBS 166.40 KX887248 KX887011 KX887129 KX886893 E. mangiferae E. mattiroloanum CBS 226.50* CBS 287.64 KX887249 KX887250 KX887012 KX887013 KX887130 KX887131 KX886894 KX886895 E. menthae CBS 322.37* KX887253 KX887016 KX887134 KX886898 E. mimosa CPC 19478* KX887255 KX887018 KX887136 KX886900 * E. oleae CBS 227.59 KX887256 KX887019 KX887137 KX886901 E. othonnae CBS 139910* = CPC 24853 N/A N/A N/A N/A E. perseae CBS 406.34* KX887258 KX887021 KX887139 KX886903 123 Author's personal copy Fungal Diversity (2019) 94:41–129 67 Table 6 (continued) Species Isolate ITS LSU RPB2 TEF1-a E. phaseoli CBS 165.31* KX887263 KX887026 KX887144 KX886908 E. piri CBS 163.29 KX887267 KX887030 KX887148 KX886912 E. pitangae CBS 227.50* KX887269 KX887032 KX887150 KX886914 E. poinsettiae CBS 109333 KX887270 KX887033 KX887151 KX886915 E. pongamiae CBS 402.63* KX887272 KX887035 KX887153 KX886917 E. populi CBS 289.64 KX887273 KX887036 KX887154 KX886918 E. proteae CPC 1349* N/A N/A N/A N/A E. protearum E. punicae CBS 113618* CPC 19968 KX887275 KX887276 KX887038 KX887039 KX887156 KX887157 KX886920 KX886921 E. quercus-ilicis CBS 232.61* KX887277 KX887040 N/A KX886922 E. randii CBS 170.38* KX887278 KX887041 KX887158 KX886923 E. rhois CBS 519.50* KX887280 KX887043 KX887160 KX886925 E. ricini CBS 403.63 = ATCC 15030 KX887281 KX887044 KX887161 KX886926 E. rosarum * CBS 212.33 KX887283 KX887046 KX887163 KX886928 E. salicina CPC 17824* KX887286 KX887049 KX887166 KX886931 E. semecarpi CBS 477.62* = ATCC 14657 KX887287 KX887050 KX887167 KX886932 E. sesseae CPC 18549 = RWB 1219 KX887288 KX887051 KX887168 KX886933 E. sicula CBS 398.59* KX887289 KX887052 KX887169 KX886934 E. solidaginis CBS 191.37* KX887290 KX887053 KX887170 KX886935 Elsinoë sp. CBS 128.14 KX887291 KX887054 KX887171 KX886936 E. tectificae CBS 124777* = CPC 14594 KX887292 KX887055 KX887172 KX886937 E. terminaliae CBS 343.39* KX887293 KX887056 KX887173 N/A E. theae E. tiliae CBS 228.50* CBS 350.73 = ATCC 24510 KX887295 KX887296 KX887058 KX887059 KX887175 KX887176 KX886939 KX886940 E. veneta CBS 164.29* = ATCC 1833 KX887297 KX887060 KX887177 KX886941 E. verbenae CPC 18561* = RWB 1232 KX887298 KX887061 KX887178 KX886942 E. violae CBS 336.35* KX887302 KX887065 KX887182 KX886946 E. zizyphi CBS 378.62* = ATCC 14656 KX887303 KX887066 KX887183 KX886947 Myriangium hispanicum CBS 247.33 KX887304 KX887067 KX887184 KX886948 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold Background Entyloma, known as the white smut fungus, was characterized by de Bary (1874). It forms teliospores with Tilletia-type basidia (holobasidia with apically produced basidiospores), and unique white coloration of the dense leaf spots caused by this pathogen. The genus was typified with E. microsporum from Ranunculus repens. The asexual genus Entylomella, described by Höhnel (1924), resembles Ramularia and was shown to be conspecific with Entyloma (Vánky 2012). Species of Entyloma have hyaline, globose, mostly smooth teliospores, embedded in the host tissue in the intercellular spaces of mesophyll cells. Prior to molecular phylogenetic studies, Entyloma species were described largely on the basis of morphology of spores and host associations. Some Entyloma species are important leaf pathogens of crops and ornamentals, including E. cosmi on Cosmos bipinnatus (Lutz and Pia˛tek 2016), E. dahliae on Dahlia sp. (Fox 2014), E. eryngii-alpini on Eryngium alpinum (Vánky 2009; Savchenko et al. 2014), E. fuscum on Papaver sp. (Vánky 2012), E. gaillardianum on Gaillardia sp. (Glawe et al. 2010; Savchenko et al. 2012; Vánky 2012) and E. helianthi on Helianthus annuus (Rooney-Latham et al. 2017). Classification—Exobasidiomycetes, Exobasidiomycetidae, Entylomatales, Entylomataceae Type species—Entyloma microsporum J. Schröt., Fungi europ. Exsicc.: no.1872 (1874) Distribution—Worldwide Disease Symptoms—Leaf spot Amphigenous circular pale green spots appear at the beginning with light to dark brown spots in the center (Garibaldi et al. 2018). Hosts—Species are e host specific and found on a variety of dicotyledonous hosts with more than 80% of the 123 Author's personal copy 68 123 Fungal Diversity (2019) 94:41–129 Author's personal copy Fungal Diversity (2019) 94:41–129 b Fig. 6 Phylogenetic tree generated by maximum Parsimony analysis of combined ITS, LSU, RPB2 and TEF1-a sequence data of Elsinoe species. Related sequences were obtained from GenBank. Seventy five strains are included in the analyses, which comprise 2479 characters including gaps. Single gene analyses were carried out (not shown) and the phylogeny generated were the same as combined analyses. Tree was rooted with Myriangium hispanicum (CBS 247.33). The maximum parsimonious dataset consisted of 1623 constant, 653 parsimony-informative and 203 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 4748 steps (CI = 0.298, RI 0.699, RC = 0.208, HI = 0.702) in the first tree. Bayesian posterior probabilities and MP bootstrap values C 50% are shown respectively near the nodes. The scale bar indicates 0.2 changes per site. The ex-type strains are in bold species occurring on asterids and ranunculoids. Entyloma species have also been recorded from other plant families, with major ones being Apiaceae, Fabaceae, Papaveraceae, Primulaceae, Saxifragaceae, Scrophulariaceae, and Solanaceae (Vánky 2012). Morphological based identification and diversity Entyloma was formerly a broad genus that included almost all of the species of smut fungi with solitary teliospores produced intercellularly in host tissue. With the advent of DNA sequence data, former Entyloma species occurring on monocots were transferred to several genera in the order Georgefischeriales (Begerow et al. 1997, 2002; Bauer et al. 2001, 2005). The number of species recognized within the genus has varied depending upon the taxonomic concept used. Morphology-based classification of Entyloma species was proposed by Savile (1947). The species were based exclusively on spore size and asexual morph. The adoption of a morphological concept dramatically decreased the number of recognized species and synonymized those with identical morphology found on the same host family. The application of this concept is challenging as it is mostly based on very simple characters (sorus morphology, size and colour of the spores, and thickness and surface of spore walls) that often overlap. Vánky in his European and World monographs of smut fungi (1994, 2012) proposed a narrower concept based on both morphological data and host-specificity. Subsequent molecular studies on the genus supported the idea that the species of Entyloma are restricted to the hosts within a single genus or species, hence the taxonomic concept proposed by Vánky proved to be more evolutionary correct than that of Savile (Begerow et al. 2002; Savchenko et al. 2014, 2015; Lutz and Pia˛tek 2016; Rooney-Latham et al. 2017; Kruse et al. 2018). However, many of the host specific species are known only from limited collections, and some have been collected only once. Therefore, the information on host specificity may change with further collections. 69 Identification of Entyloma using morphological species criteria is not always accurate, and should include molecular and host data. However, lack of DNA sequences for more than half of the known species is a problematic issue for molecular identification of the Entyloma species. Sori and spore morphology are the primary characters to identify species within this genus (Savchenko et al. 2014, 2015; Vánky 1994, 2012). However, a lot of species of Entyloma are morphologically indistinguishable and the taxonomic position of the host should be considered as another character. Molecular based identification and diversity The first phylogenetic analysis for Entyloma by Begerow et al. (2002) used ITS and LSU regions as separate genetic markers and showed that the highest resolution resulted from the analysis of ITS sequence data (Begerow et al. 2002). That study grouped all Entyloma species into two major clades, one with the species occurring on ranunculids, and another with the species from asterids. Later studies on the molecular systematics of Entyloma, focused on revealing phylogenetic relationships among particular groups of species and species complexes, supported this grouping (Savchenko et al. 2014, 2015; Lutz and Pia˛tek 2016; Rooney-Latham et al. 2017; Kruse et al. 2018). Studies applying these tools are revealing significantly greater diversity on some hosts than was previously realized. Most taxonomic studies on Entyloma using molecular data have employed ITS rDNA phylogenies, and this single marker has been shown to be reliable in species delimitation if used in combination with morphological and host data (Savchenko et al. 2014, 2015; Lutz and Pia˛tek 2016; Rooney-Latham et al. 2017). A phylogenetic tree of the genus Entyloma based on ITS data (Table 7) is presented in Fig. 7. Based on this phylogenetic tree species of Entyloma on asterids are in two major clades. Both clades include species parasitizing Asteraceae, and plants from other host families, including several members of Ranunculids and Euasterids. The results of this work are similar to previous studies on phylogenetics of Entyloma (Begerow et al. 2002; Savchenko et al. 2014, 2015; Lutz and Pia˛tek 2016; Rooney-Latham et al. 2017). Recommended genetic marker (Genus level)—ITS Recommended genetic marker (Species level)—ITS Identification of Entyloma species is complicated because of its simple morphology and often small genetic differences between species. The combination of morphology, genetic information, and host data is sufficient for identification of particular species. Accepted number of species: Currently, there are 458 Entyloma names listed in Index Fungorum (2019), but 123 Author's personal copy 70 Fungal Diversity (2019) 94:41–129 Table 7 Entyloma. Details of the isolates used in the phylogenetic analyses Species Host GenBank Accession Number (ITS) Entyloma arnicale Arnica montana AY854964 E. arnicale Arnica montana AY854965 E. arnoseridis Arnoseris minima AY081017 E. australe Physalis cordata AY081019 E. bidentis Bidens pilosa AY081020 E. browalliae Browallia americana AY081021 E. browalliae Browallia americana AY854962 E. calceolariae Calceolaria chelidonioides AY081022 E. calendulae Calendula officinalis AY081023 E. carmeli Eryngium falcatum KF310892 E. carmeli E. chrysosplenii Eryngium falcatum Chrysosplenium alternifolium KF310893 AY081024 E. chrysosplenii Chrysosplenium alternifolium AY854960 E. comaclinii Comaclinium montanum AY081025 E. compositarum Parthenium hysterophorus AY081026 E. cosmi Cosmos bipinnatus KJ728761 E. corydalis Corydalis bulbosa AY081027 E. costaricense Viguiera sp. AY081028 E. dahliae Dahlia variabilis AY854975 E. delileae Delilea biflora AY081030 E. diastateae Diastatea micrantha AY081031 E. diastateae Diastatea micrantha AY854974 E. doebbeleri Dahlia imperialis AY081032 E. doebbeleri Dahlia imperialis AY854973 E. eryngii Eryngium campestre AY081033 E. eryngii Eryngium campestre KF310897 E. eryngii E. eryngii-cretici Eryngium campestre Eryngium creticum KF310896 KF310894 E. eryngii-cretici Eryngium creticum KF310895 E. eryngii-plani Eryngium planum AY081034 E. eschscholziae Eschscholzia california KC456226 E. fergussonii Myosotis sp. AY854970 E. fergussonii Myosotis palustris AY854971 E. ficariae Ranunculs ficaria JQ586199 E. gaillardianum Gaillardia aristata AY081037 E. gaillardianum Gaillardia aristata AY854968 E. gaillardianum Gaillardia aristata GU117108 E. guaraniticum Bidens pilosa AY081038 E. hieracii Hieracium sylvaticum AY081039 E. hieracii Hieracium lachenalii AY854967 E. hieracii Hieracium murorum EU233810 E. lobeliae E. madiae Lobelia laxiflora Madia gracilis AY081042 AY081043 E. magocsyanum Tordylium cordatum KF310891 E. matricariae Tripleurospermum perforatum AY081044 E. matricariae Tripleurospermum perforatum AY854979 Ranunculus repens AY081045 Ambrosia artemisifolia AY081046 E. microsporum E. polysporum 123 * Author's personal copy Fungal Diversity (2019) 94:41–129 71 Table 7 (continued) Species Host GenBank Accession Number (ITS) E. scandicis Scandix verna KF447774 E. scandicis Scandix verna KF447775 E. zinniae Zinnia peruviana AY081049 Type species for the genus is in bold and marked with an asterisk Fig. 7 Phylogenetic tree generated from Bayesian inference based on ITS nucleotide sequence data of Entyloma species. Related sequences were obtained from GenBank. The ITS alignment included 51 sequences comprising 629 characters (including gaps). Parsimony analysis revealed that 497 characters are constant and of the variable characters 87 are parsimony-uninformative and 104 are parsimony informative. The parsimony analysis yielded 35 equally parsimonious trees, and the strict consensus tree of all equally parsimonious trees was used. The different runs of Bayesian phylogenetic analyses yielded consistent topologies. Bayesian posterior probabilities greater than 0.5 are indicated near the nodes. Numbers on branches are estimates for PPs [ 0.5. The tree is rooted with Entyloma microsporum. The type specimens are in bold about 170 were accepted in the world monograph of smut fungi by Vanky (2012) and subsequent publications dealing with this genus (Savchenko et al. 2014, 2015, 2017; Rooney-Latham et al. 2017). 123 Author's personal copy 72 References: Begerow et al. (2002), Vánky (2012), Savchenko et al. (2014, 2015), Lutz and Pia˛tek (2016), Rooney-Latham et al. (2017), Kruse et al. (2018) (morphology and phylogeny), Vánky (2012) (morphology, host specificity) Erythricium J. Erikss. & Hjortstam, Svensk bot. Tideskr. 64(2): 165 (1970) Background Erythricium was introduced by Eriksson and Hjortstam (1970) and is typified by E. laetum. Erythricium species are saprotrophic, plant pathogenic, or lichenicolous. Erythricium salmonicolor is a noteworthy pathogen of several economically important trees such as coffee, rubber, citrus, especially in tropical areas. Classification—Agaricomycetes, incertae sedis, Corticiales, Corticiaceae Type species—Erythricium laetum (P. Karst.) J. Erikss. & Hjortstam, Svensk bot. Tideskr. 64(2): 165 (1970) Distribution—Worldwide Disease Symptoms—Pink Disease Initial symptoms may vary with the host. The symptoms include production of a salmon pink mycelium on branches and stems. The mycelium spreads mainly along the underside of the branch. Leaves distal to the infection turn light green in the interveinal areas and turn scorch brown colour from the margins. Discoloration of bark, gummosis and canker on woody stems can also be observed due to the infection (Sebastianes et al. 2007). Hosts—Species of Erythricium causes pink disease on many economically important plants including Anacardium sp., Annona sp., Artocarpus sp. Camellia sp., Cinnamomum sp., Coffea sp., Eucalyptus sp., Hevea sp. Malus sp., Mangifera sp., Pyrus sp. and Theobroma cacao (Farr and Rossman 2018). Morphological based identification and diversity Erythricium currently consists of six species (Table 5) with highly similar morphology, but diverse ecology. The species share pink-coloured effused fruiting bodies with simple structure, monomitic hyphal system without clamps, flexuous basidia and large basidiospores. They inhabit a wide range of substrata (moss, dicotyledonous herb, Yucca, plant debris, and a number of fruit trees) and thrive in diverse habitats (coniferous forests, orchards, and chaparral). The significant species is the devastating plant pathogen E. salmonicolor (= Corticium salmonicolor) which is the agent of ‘pink disease’ in different tropical trees and woody plantations such as citrus, eucalypts, coffee, cacao, rubber and tea. The asexual state of the fungus has been known as Necator decretus Massee. The species was originally described from Paleotropics, but soon detected also in Neotropics as well as the areas in 123 Fungal Diversity (2019) 94:41–129 northern hemisphere influenced by tropical climates (Mordue and Gibson 1976; Sebastianes et al. 2007). Erythricium species are characterized by pink-coloured, resupinate basidiomata with monomitic hyphal system and without clamps. However, the species have highly similar micro-morphology, therefore morphology based identification may lead to confusion. Molecular based identification and diversity The latest phylogeny of Erythricium based on ITS and nLSU sequences was provided by Ghobad-Nejhad et al. (2010). The genus appears polyphyletic and its boundaries with regard to other genera in Corticiaceae (especially with Laetisaria) are unclear (Fig. 5). It seems that the trophic habit does not warrant generic delimitation in Corticiaceae (Ghobad-Nejhad 2012). Recommended genetic marker (Genus level)—nLSU (placement within Corticiaceae) Recommended genetic marker (Species level)—ITS As noted by Ghobad-Nejhad et al. (2010), the ITS sequences of the pathogenic species E. salmonicolor seem to be very divergent, and results in ambiguous alignment with other Erythricium sp. Accepted number of species: There are seven species epithets in Index Fungorum (2019) under this genus. However, only six are accepted. References: Eriksson and Hjortstam (1970) (morphology), Ghobad-Nejhad et al. (2010), Ghobad-Nejhad and Hallenberg (2011) (phylogeny). Fomitiporia Murill, N. Amer. Fl. (New York) 9(1):7 (1907) Background The genus was established by Murrill (1907). The main characters of the genus include resupinate to pileate basidiocarp, hyaline and subglobose to globose, dextrinoid and cyanophilous basidiospores, dimitic hyphal and variable cystidioles and hymenial setae (Chen and Cui 2017). The genus has been divided into two groups based on morphological characters and basidiomata habit. There are species with pileate basidiomata (e.g. F. robusta, F. erecta, F. hippophaeicola) and species sharing resupinate basidiomata (e.g., F. langloisii, F. punctata, F. pseudopunctata) (Campos-Santana et al. 2014). Fomitiporia are distributed worldwide and contain approximately 50 taxa plus numerous unidentified species (Vlasák and Kout 2011; Chen and Cui 2017; Morera et al. 2017). Fomitiporia species are pathogens and saprobes on numerous hardwood genera, for example F. mediterranea has been reported as the main agent for the esca-associated white heart rot in Europe and South Africa (Fischer 2002; Fischer and Kassemeyer 2003; Cloete et al. 2014). Fomitiporia Author's personal copy Fungal Diversity (2019) 94:41–129 australiensis, F. mediterranea, and F. punctata are associated with esca disease of grapevine (Fischer et al. 2005). Amalfi et al. (2012) introduced F. cupressicola as a parasite of living Cupressus arizonica. Disease of the Japanese pear tree (Pyrus pyrifolia var. culta) is caused by F. torreyae (Fukuta et al. 2016). Some species are an important medicinal resource e.g., F. ellipsoidea, F. hartigii, F. punctate and F. robusta (Dai et al. 2010; Zan et al. 2015; Liu et al. 2017). Classification—Agaricomycetes, Incertae sedis, Hymenochaetales, Hymenochaetaceae Type species—Fomitiporia langloisii Murill, N. Amer. Fl. (New York) 9(1):7 (1907) Distribution—Worldwide Disease Symptoms—Esca disease The initial symptoms occur on leaves as malformation and dwarfism (Fukuta et al. 2016). Dark red or white stripes occur as the foliar symptom of this disease and become yellow. Symptomatic leaves can dry completely and premature defoliation can occur. Small, circular, dark spots with a brown-purple border can be seen on fruits (Cortesi et al. 2000). Shoots and twigs die as the damage expands to the trunk. From a cross section of the trunks and large branches, light/white coloured, rotted center, surrounded by brown hard necrotic wood can be observed (Elena et al. 2006). When the disease becomes severe, decaying of the tree can be observed (Fukuta et al. 2016). Hosts—Occurs on many important plant families including Asteraceae, Fabaceae, Lamiaceae, Lauraceae, Moraceae, Myrtaceae, Oleaceae, Sapindaceae, Rosaceae and Vitaceae (Rajchenberg and Robledo 2013; Cloete et al. 2015) Morphological based identification and diversity Fiasson and Niemela (1984) redefined Fomitiporia punctata (P. Karst.) Murrill as the representative of the genus and considered F. langloisii Murrill as a synonym of Fomitiporia punctata (P. Karst.) Murrill. However, later F. langloisii was re-established as the type species based on phylogenetic analysis and herbarium studies (Decock et al. 2007). Identification of Fomitiporia has been difficult and the species were problematic and in need of clarification. The generic status of the genus was confirmed by Fischer (1996) and Dai (1999). Multi-locus phylogenetic analysis (LSU ? ITS ? TEF1a ? RPB2) combined with traditional characters were used to re-examine the classification of the genus (Amalfi et al. 2012; Chen and Cui 2017; Morera et al. 2017). Similarity of morphological characters, multi-gene phylogenetic approach and geographical distribution have been used to resolve classification problems in this genus. Recently, five species Fomitiporia alpina B.K. Cui & Hong Chen, F. gaoligongensis B.K. Cui & Hong Chen, F. hainaniana B.K. Cui & Hong Chen, F. subrobusta B.K. Cui & Hong Chen and F. subtropica B.K. Cui & Hong Chen were introduced from 73 China and F. impercepta Morera, Robledo & Urcelay was described from Argentina based on multi-gene phylogenetic analysis and morphological characterization (Chen and Cui 2017; Morera et al. 2017). In addition, Liu et al. (2018) reported F. rhamnoides T. Z. Liu & F. Wu. a novel species from China. There are 81 Fomitiporia names listed in Index Fungorum (2018), however, some of them are synonyms and some were transferred to other taxa based on phylogenetic evidence. For example F. dryophila Murrill, F. earleae Murrill, F. jamaicensis Murrill, F. laminate Murrill, F. langloisii Murrill, F. lloydii Murrill., F. maxonii Murrill, F. obliquiformis Murrill and F. tsugina Murrill were synonymized under F. punctata (P. Karst.) Murrill. Fomitiporia ellipsoidea B.K. Cui & Y.C. Dai was transferred to Phellinus ellipsoideus (Cui and Decock 2013). Some species have been rearranged into Fomitiporia; example e.g., Phellinus rosmarini Bernicchia has been recombined as Fomitiporia rosmarini (Bernicchia) Ghobad-Nejhad & Y.C. Dai (Ghobad-Nejhad and Dai 2007), while Phellinus spinescens J.E. Wright & G. Coelho was recombined as F. spinescens (J.E. Wright & G. Coelho) G. Coelho, Guerrero & Rajchenb. Phellinus uncinatus Rajchenb was transferred as F. uncinata (Rajchenb.) G. Coelho, Guerrero & Rajchenb. (Coelho et al. 2009). Basidiocarp and basidiospore characters can be used to identify this genus. However, due to inconsistency, cystidioles and hymenial setae cannot be used in species identification (Chen and Cui 2017; Liu et al. 2018). Therefore, use of DNA sequence data is crucial. Molecular based identification and diversity Classification of the genus was neglected for a long-time as Fomittiporia was considered a synonym of Phellinus (Núñez and Ryvarden 2000). Fomitiporia was confirmed to be a homogeneous genus within the Hymenochaetaceae (Zhou and Xue 2012). Recently, based on phylogenetic evidence, new species of Fomitiporia have been described and new combinations have been made into the genus (Fischer 2002; Fischer and Binder 2004; Decock et al. 2005, 2007; Fischer et al. 2005; Dai et al. 2008; Dai and Cui 2011; Amalfi et al. 2010, 2012; Zhou and Xue 2012; Amalfi and Decock 2014; Cloete et al. 2014; CamposSantana et al. 2014; Chen et al. 2016a; Vlasak and Vlasak 2016; Li et al. 2016; Chen and Cui 2017; Morera et al. 2017; Liu et al. 2018). Single gene and multigene phylogenies demonstrated that Fomitiporia is a monophyletic group (Wagner and Fischer 2001, 2002; Fischer 2002; Fischer and Binder 2004; Fischer et al. 2005; Decock et al. 2005, 2007; Larsson et al. 2006; Amalfi and Decock 2014; Campos-Santana et al. 2014). In this study we provide a phylogenetic tree (Table 8, Fig. 8) based on multi-locus phylogenetic analysis (LSU ? ITS ? TEF1-a ? RPB 2). Sequences of F. rhamnoides could not be analysed as they are unavailable in Genbank. The results from this study 123 Author's personal copy 74 provide a similar topology to those obtained by Chen and Cui (2017). There is still a need for a better marker to provide better resolution in this genus. Recommended genetic marker (Genus level)—ITS Recommended genetic markers (Species level)—LSU, ITS, TEF1-a, RPB2 Accepted number of species: There are 81 species epithets in Index Fungorum (2019) under this genus. However, 50 are accepted, but sequence data are only available for 46 species (Table 8). References: Fischer (2002), Fischer et al. (2005), Campos-Santana et al. (2014), Chen and Cui (2017), Morera et al. (2017) (morphology and phylogeny), Rajchenberg and Robledo (2013), Elena et al. (2006) (morphology, phylogeny and pathogenicity). Fulvifomes Murrill, North. Polyp.: 49 (1914) For synonyms see Index Fungorum (2019) Background Fulvifomes was described by Murrill (1914) and it is typified by F. robiniae (Murrill) Murrill. Originally, Fulvifomes was characterized by ‘‘hymenophore large, perennial, epixylous, sessile, ungulate or applanate; surface sulcate, usually anoderm and often rough or rimose; context woody or punky, brown, rarely dark-red; tubes brown, cylindric, stratose, usually thick- walled; spores smooth, ferruginous or fulvous’’ and its species were reported as growing on living hosts (Fagus, Juniperus, Quercus, Ribes, Robinia) (Murrill 1914). Wagner and Fischer (2001, 2002) redefined the genus as saprobic on deciduous wood, with resupinate, effusedreflexed or pileate, perennial basidiomata, dimitic hyphal system, ellipsoid, yellowish, IKI- basidiospores and lack of sterile elements like setae. Later, new species were described (Hattori et al. 2014; Zhou 2014, 2015; Ji et al. 2017; Salvador-Montoya et al. 2018) and a new definition of Fulvifomes was provided to include species with substipitate basidiomata with contracted base, solitary or imbricate, corky to woody hard, with pileal surface tomentose or glabrous, with or without a crust; context homogenous or duplex; hyphal system monomitic or dimitic; basidiospores subglobose to ellipsoid, yellowish to brown, fairly thick- to thick-walled, CB- or CB ? ; and occurring also on gymnosperms. Some species seem to be restricted to specific hosts, while others appear to be generalists (Murrill 1914; Larsen et al. 1985; Larsen and Cobb-poulle 1990; Sakayaroj et al. 2012; Hattori et al. 2014; Zhou 2015; Ji et al. 2017), but most host information is based on only a few collections. Classification—Agaricomycetes, incertae sedis, Hymenochaetales, Hymenochataceae Type species—Fulvifomes robiniae (Murril) Murrill, North. Polyp.: 49 (1914) 123 Fungal Diversity (2019) 94:41–129 Distribution—Cosmopolitan Disease Symptoms—White pocket rot Species of Fulvifomes develop a white pocket rot in their hosts (Larsen et al. 1985; Holmquist 1990). The pockets are irregular and appear to be interconnected by radially oriented decayed areas. The masses of fungal hyphae are white and the wood between decay pockets has a friable and crumbly texture (Larsen et al. 1985). Hosts—Acacia sp., Amburana cearensis, Anadenanthera colubrina, Apuleia leiocarpa, Aspidosperma quebracho-blanco, Bombax sp., Casuarina sp., Cedrela sp., Fagus sp., Gliricidia sp., Juniperus sp., Krugiodendron sp., Mimozyganthus carinatus, Mora gonggrijpii, Prosopis sp., Parapiptadenia rigida, Patagonula americana, Peltophorum dubium, Prunus subcoriacea, Quercus sp., Ribes sp., Robinia sp., Schinus sp., Shorea sp., Xylosma venosa, Xylocarpus sp.and Ziziphus mistol (Wright and Blumenfeld 1984; Urcelay et al. 1999; Robledo and Urcelay 2009). Morphological based identification and diversity Species of Fulvifomes were previously mostly identified as species of Phellinus sensu lato (Gilbertson and Ryvarden 1987; Larsen and Cobb-poulle 1990; Ryvarden and Gilbertson 1992; Ryvarden 2004; Dai 2010). However, when Wagner and Fischer (2001, 2002) studied the poroid Hymenochaetaceae, they resurrected several genera placed under synonymy with Phellinus, among them, Fulvifomes. Fulvifomes can be identified by the macro- and micromorphology of its basidiomata. Identification of species is not always accurate when only using morphological characters and the use of molecular data has been shown to be very useful. Molecular based identification and diversity The first phylogenetic analysis for Fulvifomes was carried out by Wagner and Fischer (2001, 2002) when studying the poroid Hymenochaetaceae. The authors used sequence data from the LSU rDNA and recovered Fulvifomes among Phellinus species. Latter, Zhou (2014, 2015), Ji et al. (2017) and Salvador-Montoya et al. (2018) described new species using both LSU rDNA and ITS sequence data, in separate or combined analyses. Here we reconstruct the phylogeny of Fulvifomes (Table 9, Fig. 9) based on the combined analyses of ITS and LSU rDNA sequence data. This tree includes a reference sequence of the type species of the genus, collected in the same country and on the same host, and the sequence of the type of newly described F. squamosus Salvador-Montoya & Drechsler-Santos (Salvador-Montoya et al. 2018) and provides the first sequence of F. rhytiphloeus (Mont.) Camp.-Sant. & Robledo. Additionally, the tree implies the absence in the Americas of F. fastuosus (Lév.) Bondartseva & S. Herrera, F. merrillii (Murrill) Baltazar & Gibertoni and F. nilgheriensis (Mont.) Bondartseva & S. Herrera, Author's personal copy Fungal Diversity (2019) 94:41–129 75 Table 8 Fomitiporia. Details of the isolates used in the phylogenetic analyses Species Isolate LSU ITS TEF1-a RPB2 Fomitiporia aethiopica MUCL 44777* AY618204 GU478341 GU461893 JQ087956 F. alpina Dai 15735 KX639645 KX639627 KX639664 KX639680 F. apiahyna MUCL 51451 GU461997 GU461963 GU461896 JQ087958 F. atlantica FLOR 58554 KU557526 KU557528 – – F. australiensis MUCL 49406 GU462001 AY624997 GU461897 JQ087959 F. baccharidis MUCL 47756 JQ087913 JQ087886 JQ087940 JQ087993 F. bakeri FP-134784-Sp JQ087901 JQ087874 JQ087928 JQ087960 F.bannaensis MUCL 45926 EF429217 GU461942 GU461898 JQ087961 F. calkinsii MUCL 51095 KF444708 KF444685 KF444754 KF444731 F. capensis MUCL 53009 JQ087917 JQ087890 JQ087944 JQ087997 F. castilloi MUCL 53481* JQ087916 JQ087889 JQ087943 JQ087996 F. cupressicola MUCL 52486* JQ087904 JQ087877 JQ087931 JQ087965 F. deserticola PRM 934073 – KT381632 – – F. dryophila TJV-93-232 EF429221 EF429240 GU461902 JQ087969 F. erecta MUCL 49871 GU461976 GU461939 GU461903 JQ087971 F. expansa MUCL 55026 KJ401032 KJ401031 KJ401033 KJ401034 F. fissurata PRM922626 – KT381627 – – F. gabonensis MUCL 47576* GU461990 GU461971 GU461923 JQ087972 F. gaoligongensis Cui 8261 KX639642 KX639624 KX639663 KX639678 F. hainaniana CL06-372 KX639654 KX663826 KX639660 – F. hartigii MAFF 11–20016 JQ087909 JQ087882 JQ087936 JQ087975 F. hippophaëicola MUCL 31746 AY618207 GU461945 GU461904 JQ087976 F. impercepta CORDC00005289 MF615266 MF615298 – – F. ivindoensis MUCL 51312* GU461978 GU461951 GU461906 JQ087979 F. langloisii MUCL 46375 EF429225 EF429242 GU461908 JQ087980 F. maxonii MUCL 46017 EF429230 EF433559 GU461910 JQ087983 F. mediterranea MUCL 45670 GU461980 GU461954 GU461913 JQ087985 F. neotropica MUCL 51335* KF444721 KF444698 KF444771 KF444744 F. nobilissima MUCL 51289* GU461984 GU461965 GU461920 JQ087987 F. norbulingka Cui 9770 KU364430 KU364420 KU364433 – F. pentaphylacis Yuan 6012 JQ003901 JQ003900 KX639671 KX639683 F. polymorpha MUCL 46166 DQ122393 GU461955 GU461914 JQ087988 F. pseudopunctata MUCL 51325 GU461981 GU461948 GU461916 JQ087998 F. punctata MUCL 34101 AY618200 GU461947 GU461917 JQ088000 F. punicata Cui 23 GU461991 GU461974 GU461927 JQ088002 F. robusta CBS 389.72 JQ087919 JQ087892 JQ087946 JQ088004 F. sonorae MUCL 47689 JQ087920 JQ087893 JQ087947 JQ088006 F. subhippophaëicola Cui 12096 KU364426 KU364421 KU364437 – F. subrobusta Dai 13576 KX639635 KX639617 KX639655 KX639672 F. subtilissima FURB47557 KU557527 KU557531 KU557532 KU557533 F. subtropica Cui 9122 KX639640 KX639622 KX639661 KX639677 F. tabaquilio MUCL 46230 DQ122394 GU461940 GU461931 JQ088008 F. tenuis MUCL 44802* AY618206 GU461957 GU461934 JQ088010 F. tenuitubus Dai 16204 KX639637 KX639619 KX639657 KX639674 F. texana MUCL 47690 JQ087921 JQ087894 JQ087948 JQ088013 F. torreyae MUCL 47628 JQ087923 JQ087896 JQ087950 JQ088015 F. tsugina MUCL 52702 JQ087925 JQ087898 JQ087952 JQ088017 F. rhamnoides Dai 18091 MH234392 MH234389 – – Phellinus uncisetus (out group) MUCL 46231 EF429235 GU461960 GU461937 JQ088020 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher stains are in bold 123 Author's personal copy 76 Fungal Diversity (2019) 94:41–129 Fig. 8 Phylogenetic tree generated by maximum Parsimony analysis of combined nLSU, ITS, TEF1-a and RPB2 sequence data of Fomitiporia species. Related sequences were obtained from GenBank. Forty five strains are included in the analyses, which comprise 3836 characters including gaps. Tree was rooted with Phellinus uncisetus (MUCL 46231). The maximum parsimonious dataset consisted of 2537 constant, 841 parsimony-informative and 458 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of six equally most parsimonious trees with a length of 3416 steps (CI = 0.511, RI = 0.598, RC = 0.305, HI = 0.489) in the first tree. Bayesian posterior probabilities and MP bootstrap values C 50% are shown respectively near the nodes. The scale bar indicates 10 changes per site. The ex-type strains are in bold whose type localities are in Asia, and also implies the wider distribution of F. kawakamii (M.J. Larsen, Lombard & Hodges) T. Wagner & M. Fisch., previously thought to be endemic to Hawaii (EUA, Larsen et al. 1985) (99% similarity and 89% query cover with F. kawakamii AY059028 from the type locality, LSU only), and probably identified as F. nilgheriensis (CBS 209.36) or F. fastuosus (other specimens collected in the Americas). 123 Recommended genetic marker (Genus level)—LSU Recommended genetic markers (Species level)—ITS, TEF1-a and RPB2 as additional markers Matheny et al. (2007) studied the level of resolution of TEF1-a and RPB2 in phylogeny of Basidiomycota, Author's personal copy Fungal Diversity (2019) 94:41–129 Table 9 Fulvifomes. Details of the isolates used in the phylogenetic analyses 77 Species Voucher LSU ITS F. centroamericanus JV0611-8P – KX960757 F. centroamericanus JV0611-III* KX960764 KX960763 F. fastuosus LWZ 20140731-13 KR905668 KR905674 F. fastuosus CBS 213.36 AY059057 AY558615 F. fastuosus LWZ 20140801-1 KR905669 KR905675 F. fastuosus UOC DAMIA D27b – KJ206286 F. fastuosus LWZ 20140728-29 – KR905673 F. fastuosus UOC KAUNP K20 – KR867659 F. grenadensis JV1212/2 J – KX960756 F. grenadensis 1607/66 F. grenadensis JRF74 MH048087 MH048097 F. grenadensis PH6 MH048086 MH048096 KC879263 KX960758 F. hainanensis Dai 11 573* JX866779 F. halophilus XG4 JX104752 JX104705 F. imbricatus F. imbricatus LWZ 20140728-16* LWZ 20140729-26 KR905670 KR905671 KR905677 KR905679 F. indicus O 25034 KC879259 KC879262 F. indicus Yuan 5932 JX866777 KC879261 F. kawakamii PPT152 MH048085 MH048095 F. kawakamii AS1733 MH048083 MH048093 F. kawakamii AS615 MH048082 MH048092 F. kawakamii AS2486 MH048084 MH048094 F. kawakamii CBS 428.86 AY059028 – F. krugiodendri JV0904-1* KX960765 KX960762 F. krugiodendri JV0312-24 KX960760 KX960766 F. merrillii PM950703-1 – EU035313 F. merrillii PM950703-1 – EU035310 F. merrillii – – JX484013 F. nilgheriensis CBS 209.36 AY059023 AY558633 F. rhytiphloeus AMO763 MH048081 MH048091 F. robiniae F. siamensis CBS 211.36 XG2 – JX104756 AY558646 JX104709 F. squamosus CS456* MF479266 MF479267 F. squamosus CS385 MF479265 MF479268 F. squamosus CS444 MF479264 MF479269 F. thailandicus LWZ 20140731-1* KR905665 KR905672 F. xylocarpicola BBH 28342 JX104723 JX104676 Fulvifomes sp. S2T26M1 JX104754 JX104707 Fulvifomes sp. KBXG3 – JX104706 Fulvifomes sp. KP311 – KP658651 Fulvifomes sp. KP305A – KP658646 Ex-type (ex-epitype) strains are in bold and marked with an * concluding that RPB2 is more efficient to resolve both higher and lower clades, while TEF1-a is better to solve the phylogeny in high taxonomic levels. Considering rDNA markers, LSU rDNA is used for genera delimitation, while ITS rDNA is used to delimit species (James et al. 2006; Matheny et al. 2007; Öpik et al. 2010; Schoch et al. 2012). In Hymenochataceae, these two regions are extensively used in many phylogenies, to discriminate taxa in the family (Wagner and Fischer 2001, 2002; Larsson et al. 2006). In Fulvifomes, many studies used sequences from ITS and LSU rDNA as markers (Zhou 2014, 2015; Ji et al. 2017; Salvador-Montoya et al. 2018). However, TEF1-a 123 Author's personal copy 78 Fungal Diversity (2019) 94:41–129 Fig. 9 Phylogenetic tree generated by Bayesian inference (BI) of combined ITS and LSU rDNA sequence data of Fulvifomes species. Forty samples are included in the analyses, which comprise 1224 characters including gaps. Tree was rooted with Fomes fomentarius (DAOM129034) and Amyloporia carbonica (Wilcox-96). Tree topology of the BI was similar to the maximum likelihood (ML) analysis (Figure not shown). The matrix had 1021 phylogenetic informative sites (83, 42%). Estimated base frequencies were as follows; A = 0.241, C = 0.208, G = 0.280, T = 0.271; substitution rates AC = 0.768, AG = 4.476, AT = 1.569, CG = 1.133, CT = 8.068, GT = 1.000; gamma distribution shape parameter a = 0.246. Bayesian posterior probabilities and ML bootstrap values C 50% are shown respectively near the nodes. The scale bar indicates 0.05 changes per site. Sequences generated in this study and of the types are in bold and RPB2 are also being used for delimitation of taxa of poroid Hymenochaetaceae, for instance in Fomitiporia and Phellinus (Amalfi et al. 2010, Amalfi and Decock 2014; Campos-Santana et al. 2014, 2016; Chen and Cui 2017; Morera et al. 2017). Accepted number of species: There are 58 species epithets in Index Fungorum (2019) under this genus. However, 24 are accepted. 123 References: Wagner and Fischer (2001, 2002) (phylogeny), Hattori et al. (2014) (morphology), Zhou (2014, 2015), Ji et al. (2017), Salvador-Montoya et al. (2018) (morphology, phylogeny). Laetisaria Burds., Trans. Br. Mycol. soc. 72(3): 420 (1979) Author's personal copy Fungal Diversity (2019) 94:41–129 Background The genus Laetisaria was established by Burdsall (1979) for L. fuciformis (asexual Isaria fuciformis) with effuse, whitish pink fruiting bodies, causing red thread disease in turfgrasses. Each of the other three species assigned to Laetisaria represents a different trophic habit: L. agaves is saprotrophic, L. arvalis is a mycoparasite and L. lichenicola is lichenicolous. Laetisaria arvalis is soil-inhabiting and has been proposed as a biocontrol agent against some fungal pathogens such as Pythium and Rhizoctonia. Classification—Agaricomycetes, incertae sedis, Corticiales, Corticiaceae Type species—Laetisaria fuciformis (Berk.) Burds., Trans. Br. Mycol. Soc. 72(3): 420 (1979) Distribution—Europe, N. America, Australasia. Disease Symptoms—Red thread Small water-soaked spots covering a large portion of the grass leaf can be observed. Infected grass blades soon die and fade to a bleach-tan colour (Smiley et al. 2005). Hosts—Turf grasses Morphological based identification and diversity Laetisaria currently contains four species (Index Fungorum 2018; Table 5). However as stated by the authors, due to the taxonomic confusion, the species have been placed only tentatively in Laetisaria. Laetisaria agaves and L. lichenicola are sexual morph only, while L. arvalis and L. fuciformis produce asexual morphs as well. Molecular based identification and diversity The species of Laetisaria do not form a monophyletic clade in phylogenetic studies. The generic type L. fuciformis groups with several Marchandiomyces species and Limonomyces, while L. arvalis shows affinity to Waitea circinata (Fig. 5). Laetisaria lichenicola was recently described for a lichen parasite forming resupinate, pink fruiting bodies on lichen talli (Diederich et al. 2011). The ongoing taxonomic reconsideration of genera in Corticiaceae would help resolve the phylogeny of Laetisaria and allies (Ghobad-Nejhad et al., unpublished). Recommended genetic marker (Genus level)—nLSU Recommended genetic marker (Species level)—ITS Accepted number of species: Four species References: Burdsall (1979) (morphology), Diederich et al. (2011) (morphology, phylogeny). Limonomyces Stalpers & Loer., Can. J. Bot. 60(5):553 (1982) Background Limonomyces was introduced by Stalpers and Loerakker (1982) and is typified with L. roseipellis, causing pink 79 disease in turf grasses. As in many Corticiaceae, the species forms thin, effused pink-coloured fruiting bodies with a simple microstructure. The second species L. culmigenus also causes pink disease on grasses, but with less obvious disease symptoms. Classification—Agaricomycetes, incertae sedis, Corticiales, Corticiaceae Type species—Limonomyces roseipellis Stalpers & Loer., Can. J. Bot. 60(5):553 (1982) Distribution –Britain, Canada, China, Italy, the Netherlands, US Disease Symptoms—Pink Patch Disease In the early stage of infection, symptoms appear as small blighted areas on leaves that enlarge rapidly to cover most of the leaf blade. Affected leaves dry out and fade to a bleached straw colour, appearing as irregular-shaped patches on blighted grasses. During moist weather, leaves are covered with pink mycelium (Maccaroni et al. 2002; Burpee et al. 2003; Zhang et al. 2013). Hosts—Poaceae Morphological based identification and diversity Limonomyces comprises two species (Index Fungorum 2019; Table 5), morphologically differing in their spore size and number of strigmata. The species are distributed in the northern hemisphere. While L. culmigenus is rare, the generic type has a wider distribution. Molecular based identification and diversity The affinity of Limonomyces to some genera in Corticiales such as Vuilleminia and Galzinia was discussed in its original description. Limonomyces species are nested in a clade containing Laetisaria and several asexual Marchandiomyces, but the two species in the genus do not form a monophyletic clade (Fig. 5). Recommended genetic marker (Genus level)—nLSU (confident placement in Corticiaceae) Recommended genetic marker (Species level)—ITS Accepted number of species: Two species References: Maccaroni et al. (2002) (morphology); Burpee et al. (2003) (pathogenicity); Zhang et al. (2013) (morphology, phylogeny and pathogenicity) Neofabraea H.S. Jacks., Rep. Oregon Exp. Sta.: 187 (1913) [1911–1912] For synonyms see Index Fungorum (2019) Background Neofabraea was introduced by Jackson (1913) and typified by N. malicorticis. Neofabraea alba, N. kienholzii, N. malicorticis and N. perennans are pathogens, saprobes or endophytes mostly associated with fruits. Neofabraea 123 Author's personal copy 80 are known as the causal agent of bull’s eye rot of apple and pear fruit, which is an important postharvest disease in the Pacific Northwest of the USA, and also occurs in Australia, Canada, Chile, Europe and New Zealand (de Jong et al. 2001; Cunnington 2004; Henriquez et al. 2004; Gariepy et al. 2005; Henriquez 2005; Johnston et al. 2005; Spotts et al. 2009; Soto-Alvear et al. 2013). The Neofabraea complex also cause anthracnose canker and perennial canker on pome trees (Verkley 1999; de Jong et al. 2001; Henriquez et al. 2006), canker on Populus sp. (Thompson 1939; Roll-Hansen and Roll-Hansen 1969; Kasanen et al. 2002), coin canker of ash (Rossman et al. 2002), fruit rot on kiwifruit (Johnston et al. 2004), fruit spot on olive (Rooney-Latham et al. 2013), and leaf spot on citrus (Zhu et al. 2012). Classification—Leotiomycetes, Leotiomycetidae, Helotiales, Dermataceae Type species—Neofabrea malicorticis (Cordley) H.S. Jacks., Rep. Oregon Exp. Sta.: 187 (1913) [1911–1912] Distribution—Worldwide Disease Symptoms—Anthracnose and perennial canker, Bulls’ eye rot, Fruit rot Bulls’ eye rot (mainly caused by N. alba, N. kienholzii and N. perennans) lesion is circular, flat to slightly sunken and appears light brown to dark brown with a light coloured centre on fruits (Spotts et al. 2009). Anthracnose cankers caused by N. alba, N. malicorticis and N. perennans appear as small circular spots that are reddish when moist. These lesions become elongated and sunken as they enlarge and orange to brown, with cracks around the edges. As damaged bark disintegrates, the canker develops a ‘‘fiddle string’’ appearance. Perennial canker is very similar to the young anthracnose canker. Sunken, elliptical, discoloured areas in the bark can be observed. As the cankers age, formation of callus tissue will results in a series of concentric rings (Henriquez et al. 2006). Hosts—Actinidia sp., Aucuba sp., Chamaecyparis sp., Ilex sp., Malus sp., Olea sp., Populus sp., Pyrus sp. Morphological based identification and diversity Neofabraea was introduced based on Neofabraea malicorticis (Jackson 1913). This genus is very similar to Pezicula and Nannfeldt (1932) combined the type species N. malicorticis into Pezicula. Some other Neofabraea species were transferred to Pezicula (Seaver 1951; Dugan et al. 1993). With new morphological information and phylogenetic analyses, Neofabraea and Pezicula species were retained in separate genera (Verkley 1999; Abeln et al. 2000), but Pezicula alba resembles Neofabraea alba and was hence synonymised to Neofabraea alba (Verkley 1999). In previous studies the asexual morphs of Neofabraea have been reported to be Cryptosporiopsis with aseptate, fusiform conidia (and later often septate) (Verkley 123 Fungal Diversity (2019) 94:41–129 1999; Johnston et al. 2004; Zhu et al. 2012). To avoid dual nomenclature, species of Cryptosporiopsis have been transferred to Neofabraea. To protect Neofabraea over Phlyctema, a suggestion was made to combine Neofabraea vagabunda under N. alba (Johnston et al. 2014). In the past, the type of species of Neofabrae was confused with Neofabraea perennas. In North America these two were considered as different species but in Europe they were considered as the same. Based on multigene phylogenetic analyses, de Jong et al. (2001) provided data to prove that these two taxa were different by vegetative compatibility, canker symptoms and response to chemical treatments. Usually the apothecia of Neofabraea and Pezicula are similar, but excipular tissues in Pezicula are less different from Neofabraea (Verkley 1999) and macroconidia of Neofabraea are more strongly curved, but the basal scar is smaller than Pezicula. In Pezicula, there are two types of conidiogenous cells, determinate and phialidic or indeterminate and proliferating percurrently, but in Neofabraea only phialidic conidiogenous cells are found (Chen et al. 2016b). These characters can be used in differentiating these two genera. However, as morphological variation among the species of Neofabrea is limited, identification of species based soley on morphological characters are not encouraged. Molecular based identification and diversity Neofabraea perennans was described and moved to Pezicula by Dugan et al. (1993). Multigene phylogenetic analyses (ITS nuclear rDNA, SSU mitochondrial rDNA, TUB2) indicated that Neofabraea can be separated from Pezicula (de Jong et al. 2001). Moreover, the TUB2 gene phylogenies showed that apple pathogens contain four clades with strong support, i.e., N. alba, N. krawtzewii, N. malicorticis and N. perennans (de Jong et al. 2001). Although Index Fungorum (2019) lists 14 species in this genus, only nine species, N. actinidiae, N. alba, N. brailiensis, N. inaequalis, N. kienholzii, N. krawtzewii, N. malicorticis, N. perennans and N. vagabunda have sequence data. Therefore, fresh collections and sequence data are needed for the other species. This study reconstructs the phylogeny of Neofabrea based on analyses of a combined ITS, LSU, RPB2 and TUB2 sequence data (Table 10, Fig. 10). The phylogenetic tree obtained corresponds to previous studies (Chen et al. 2016b; de Jong et al. 2001). Recommended genetic marker (Genus level)—LSU Recommended genetic marker (Species level)—TUB2 TUB2 gene is the best single genetic marker for the genus Neofabraea, but combined ITS, LSU, RPB2 and TUB2 sequence data can resolve almost all species of Neofabraea (Chen et al. 2016b). Author's personal copy Fungal Diversity (2019) 94:41–129 Table 10 Neofabraea. Details of the isolates used in the phylogenetic analyses 81 Species Isolate ITS LSU RPB2 Btub Neofabraea actinidiae CBS 194.69 – KR858871 KR859320 KR859286 N. actinidiae CBS 121403 – KR858870 KR859319 KR859285 N. alba ATCC 38338 AF281366 – – AF281456 N. alba CBS 452.64 – – – AF281457 N. brasiliensis CNPUV499* KR107002 – – KR107011 N. brasiliensis CNPUV506 KR107001 – – KR107010 N. inaequalis CBS 326.75 KR859081 KR858872 KR859321 KR859287 N. kienholzii CBS 126461 KR859082 KR858873 KR859322 KR859288 N. kienholzii CBS 318.77 KR859083 KR858874 KR859323 KR859289 N. krawtzewii CBS 102867 KR859084 KR858875 KR859324 AF281459 N. krawtzewii CBS 102868 – – – KR866108 N. malicorticis CBS 102863 KR859085 KR858876 KR859325 KR859290 N. malicorticis CBS 122030 NR144926 KR858877 KR859326 KR859291 N. perennans CBS 102869 KR859087 KR858878 KR859327 KR866100 N. perennans N. perennans CBS 275.29 CBS 453.64 KR859088 KR859089 KR858879 KR858880 KR859328 KR859329 KR859292 KR866102 N. vagabunda M888 – – – KT963932 Pezicula carpinea CBS 923.96 KR859108 KR858899 KF376158 KF376279 P. carpinea CBS 921.96 KR859107 KR858898 KF376159 KF376278 P. acericola CBS 239.97 KR859093 KR858884 KF376214 KF376283 P. brunnea CBS 120291 KR859103 KR858894 – – P. aurantiaca CBS 201.46 KR859102 KR858893 KF376210 KF376335 Dermea cerasi KUS-F50981* – JN086690 – – Parafabraea eucalypti CBS 124810 KR859091 GQ303310 KR859331 KR859294 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher stains are bolded Accepted number of species: There are 14 species epithets in Index Fungorum (2019) under this genus. However, nine species with molecular data are accepted. References: Verkley (1999) (morphology and pathogenicity), de Jong et al. (2001), Chen et al. (2016b) (phylogeny), Wang et al. (2015a, b) (morphology and key to species) Phaeoacremonium W. Gams, Crous & M.J. Wingf., Mycologia 88(5):789 (1996) For synonyms see Index Fungorum (2019) Background The hyphomycetous genus Phaeoacremonium was established by Crous et al. (1996) to accommodate six species with P. parasiticum (Ajello, Georg & C.J.K. Wang) W. Gams, Crous & M.J. Wingf. as the type, which was transferred from the genus Phialophora Medlar. It is morphologically similar to Acremonium Link and Phialophora Medlar, but can be distinguished from them by its aculeate phialides and inconspicuous, non-flaring collarettes and pigmented vegetative hyphae (Crous et al. 1996). The genus Phaeoacremonium together with Togninia Berl. were accommodated in the family Togniniaceae Réblová, L. Mostert, W. Gams & Crous and in the order Togniniales Senan., Maharachch. & K.D. Hyde (Maharachchikumbura et al. 2015). Gramaje et al. (2015) reduced Togninia to synonymy with Phaeoacremonium as 13 of 26 epithets are insufficiently known and some already have names in Phaeoacremonium. Currently, only Phaeoacremonium is retained in Togniniaceae (Wijayawardene et al. 2018). Classification—Sordariomycetes, Diaporthomycetidae, Togniniales, Togninicaceae Type species—Phaeoacremonium parasiticum (Ajello, Georg & C.J.K. Wang) W. Gams, Crous & M.J. Wingf., Mycologia 88(5):789 (1996) Distribution—Worldwide Disease Symptoms—Brown wood streaking/Esca Phaeoacremonium species are known as vascular plant pathogens causing wilting and dieback of several woody plants, e.g. P. fuscum L. Mostert, Damm & Crous, P. pallidum Damm, L. Mostert & Crous and P. prunicola L. Mostert, Damm & Crous which were isolated from necrotic woody tissue (Damm et al. 2008). Yellowing, wilting, dieback, canker and internal node discoloration can be 123 Author's personal copy 82 Fungal Diversity (2019) 94:41–129 Fig. 10 Phylogenetic tree generated by maximum Parsimony analysis of combined ITS, LSU, RPB2 and TUB2 sequence data of Neofabraea species. Related sequences were obtained from GenBank. Twenty four strains are included in the analyses, which comprise 2767 characters including gaps. Single gene analyses were carried out (not shown) and the phylogeny generated were the same as combined analyses. Tree was rooted with Parafabraea eucalypti (CBS 124810). The maximum parsimonious dataset consisted of constant 2153, 463 parsimony-informative and 151 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of two equally most parsimonious trees with a length of 1023 steps (CI = 0.742, RI 0.825, RC = 0.612, HI = 0.258) in the first tree. Maximum parsimony bootstrap support values C 50% (BT) are shown respectively near the nodes. The scale bar indicates 40.0 changes per site. The ex-type strains are in bold observed from the trees that are affected by the species of this genus (Cloete et al. 2011; Mohommadi et al. 2013; Úrbez-Torres et al. 2014). In cross section of affected wood, wedge shaped and circular wood necrosis can be observed (Sami et al. 2014). Some species also cause human diseases, e.g. P. parasitica Ajello, Georg & C.J.K. Wang was described from a subcutaneous infection of a human patient (Ajello et al. 1974; Baddley et al. 2006). Considering its association with human infections and disease symptoms of several woody hosts, it is represented as an ecologically important group of fungi (Crous et al. 1996). Hosts—Woody plants with brown wood streaking, humans with phaeophyphomycotic infections, larvae of bark beetle, arthropods and soil. Species of Phaeoacremonium are associated with more than 50 plant genera. 123 Morphological based identification and diversity To date, there are 65 epithets recorded in Index Fungorum (2019). Six species of Phaeoacremonium, i.e. P. aleophilum, P. angustius, P. chlamydosporum, P. inflatipes, P. parasiticum and P. rubrigenum, were originally identified based on morphological features (Crous et al. 1996) and a key based on morphological and cultural characters was also provided, but some species were reported to have been misidentified. For instance, Phaeoacremonium chlamydosporum W. Gams, Crous, M.J. Wingf. & Mugnai was referred to a new genus, Phaeomoniella Crous & W. Gams based on its straight, Author's personal copy Fungal Diversity (2019) 94:41–129 pigmented conidia, dark green–brown conidiophores with light green to hyaline conidiogenous cells, a yeast-like growth in young colonies, a Phoma-like synanamorph, and producing chlamydospore-like structures in culture (Gams and Crous 2000). Subsequently, Mostert et al. (2005) reexamined all isolates of P. inflatipes and revised their taxonomy based on morphology and sequence data. Because of numerous incorrect identifications that have been made since 1996 (Crous et al. 1996; Gams and Crous 2000), it is difficult to use the key provided by Crous et al. (1996) for identification (Mostert et al. 2005). An updated multiple-entry electronic key was developed by Mostert et al. (2005). During 2006–2018, about 36 new species were described, most of which were identified based on DNA sequence data (Gramaje et al. 2009, 2014, 2015; Ariyawansa et al. 2015b; Crous et al. 2016). Mostert et al. (2005) suggested that a combination of macromorphological characters (including colonial colour, growth rate, maximum growth temperature and sometime the size and extent of mycelial warts can be distinguishing features in several species as well) and micromorphological characters (including conidiophores, phialides type, to a less extent the shape of conidia) proved useful in identification. The representative features are warty mycelium, pigmented conidiophores with phialidic conidiogenous cells and hyaline, aseptate conidia which vary from oblongellipsoidal to allantoid in shape. Normally the conidia gather in slimy heads at phialide apices (Gramaje et al. 2015). However, minor differences in cultural and microscopic features also cause misidentification for several species (Mostert et al. 2005). Therefore, molecular data is necessary to deeply understand these species. Molecular based identification and diversity Presently, Phaeoacremonium has been reported to represent a monophyletic group of taxa (Gramaje et al. 2015). There have been studies done to investigate phylogenetic relationships among a large number of species. Mostert et al. (2006) provided a rapid identification method for 22 species of Phaeoacremonium with 23 species-specific primers. It facilitates the understanding of indiscernible species in plant as well as in human disease, however, is the key still needs to be validated. Phylogenetic analysis based on individual LSU and SSU sequence data have good performance in study of generic placement. Analyses showed that Phaeoacremonium species form a distinct clade within Sordariomycetes and have close affinity with Diaporthales and Calosphaeriales species (Mostert et al. 2003; Damm et al. 2008; Gramaje et al. 2015; Crous et al. 2016). Herewith, we update the phylogenetic relationship of Phaeoacremonium species by analysing concatenated alignment of TUB2 and ACT sequence data (Table 11, Fig. 11). Molecular data of three species are not included 83 in the phylogenetic analysis; for P. aquaticum and P. leptorrhynchum only ITS is available, for P. inconspicuum no ex-type culture or DNA sequence data exist (Gramaje et al. 2015). In the phylogenetic tree, three distinct clades were observed, and the topological structure is accordance with Silva et al. (2017). Recommended genetic markers (Genus level)—SSU, LSU Recommended genetic markers (Species level)—ACT, TUB2 Multigene phylogeny gives deeper understanding in the phylogenetic relationships of Phaeoacremonium species. For example, combined ITS- TEF1-a - regions (Mostert et al. 2003), combined ITS-TUB2-ACT-TEF1-a dataset (Úrbez-Torres et al. 2014) and combined ACT-TUB2 regions can resolve intraspecific identification; of which ACT-TUB2 sequence data analysis was frequently used for the investigation of taxonomy and diversity among Phaeoacremonium as it provides topologies with greater resolution and well supported (Damm et al. 2008, Essakhi et al. 2008, Gramaje et al. 2015, Silva et al. 2017, Spies et al. 2018). Accepted number of species: There are 65 species epithets in Index Fungorum (2019) under this genus. However, 62 are accepted. This is because P.aleophilum and P. mortoniae were treated as basionym of P. minimum and P. fraxinopennsylvanicum, respectively (Gramaje et al. 2015). Phaeoacremonium chlamydosporum was transferred to a new genus, Phaeomoniella (Gams and Crous 2000). References: Crous et al. (1996) (morphology and a key for Phaeoacremonium species), Mostert et al. (2005) (morphology, phylogeny and a key for Phaeoacremonium species), Úrbez-Torres et al. (2014) (detection, morphology, phylogeny and pathogenicity), Gramaje et al. (2015), Maharachchikumbura et al. (2016) (morphology and phylogeny). Phellinotus Drechsler-Santos et al., in Drechsler-Santos et al., Phytotaxa 261(3): 222 (2016) Background Phellinotus was described by Drechsler-Santos et al. (2016) and it is typified by Phellinotus neoaridus Drechsler-Santos & Robledo. Only two species, P. neoaridus and P. piptadeniae (Teixeira) Drechsler-Santos & Robledo have been reported, mostly on living members of Fabaceae (Drechsler-Santos et al. 2010, 2016; Salvador-Montoya et al. 2015). Phellinotus is characterized by the annual to perennial, pileate, applanate to ungulate, fulvous brown to dark brown basidiomata; brown to blackened, rugose to rimose pileus; context with a black line near/below the upper surface, distinct or indistinct; and stratified tubes, with or without contextual tissue layer between them. The 123 Author's personal copy 84 Fungal Diversity (2019) 94:41–129 Table 11 Phaeoacremonium. Details of the isolates used in the phylogenetic analyses Species Isolate Phaeoacremonium. africanum CBS 120863 = STE-U 6177* EU128100 EU128142 P. album BS 142688 = STE-U 8379 = PMM1938* KY906885 KY906884 CBS 142689 = STE-U 8378 = PMM2275 KY906925 KY906924 P. aleophilum = P. minimum CBS 246.91* AF246811 AY735497 CBS 100397 AF246806 AY735498 CBS 110034* AY579301 AY579234 CBS 729.97 AY579302 AY579235 P. amstelodamense CBS 110627* AY579295 AY579228 P. amygdalinum CBS 128570 = Psp-3* JN191307 JN191303 Psp-1 JN191305 JN191301 CBS 114992* DQ173104 DQ173127 CBS 114991 DQ173103 DQ173126 DQ173135 P. alvesii P. angustius TUB2 Actin P. argentinense CBS 777.83* DQ173108 P. armeniacum ICMP 17421* EU596526 EU595463 P. aureum CBS 142690 = STE-U 8374 = CSN1322 KY906799 KY906798 CBS 142691 = STE-U 8372 = CSN23* KY906657 KY906656 P. australiense CBS 113589* AY579296 AY579229 CBS 113592 AY579297 AY579230 P. austroafricanum CBS 112949* DQ173099 DQ173122 CBS 114994 DQ173102 DQ173125 P. bibendum CBS 142694 = STE-U 8365 = CSN894* KY906759 KY906758 P. canadense PARC327* KF764651 KF764499 P. cinereum CBS 123909 = Pm5* FJ517161 FJ517153 Pm4 FJ517160 FJ517152 P. croatiense CBS 123037 = 113Pal* EU863482 EU863514 P. fraxinopennsylvanicum = P. mortoniae CBS 110212 DQ173109 DQ173136 P. fraxinopennsylvanica CBS101585* KF764684 DQ173137 P. fuscum CBS 120856 = STE-U 5969* EU128098 EU128141 P. gamsii CBS 142712 = STE-U 8366 = CSN670* KY906741 KY906740 P. geminum CBS 142713 = STE-U 8402 = C741 = CSN1944* KY906649 KY906648 CBS 142717 = STE-U 8367 = C631 = CSN1945 KY906647 KY906646 P. globosum ICMP 16988* EU596525 EU595466 ICMP 16987 EU596527 EU595459 P. griseo-olivaceum CBS 120857 = STE-U 5966* EU128097 EU128139 P. griseorubrum CBS 111657* AY579294 AY579227 CBS 566.97 AF246801 AY579226 P. hispanicum CBS 123910 = Pm8* FJ517164 FJ517156 P. hungaricum CBS 123036 = 90Pal* EU863483 EU863515 P. inflatipes CBS 391.71* AF246805 AY579259 CBS 113273 AY579323 AY579260 P. iranianum CBS 101357* DQ173097 DQ173120 CBS 117114 DQ173098 DQ173121 P. italicum CBS 137763 = Pm19* KJ534074 KJ534046 CBS 137764 = Pm20 KJ534075 KJ534047 CBS 142695 = STE-U 8398 = CSN13 KY906651 KY906650 CBS 142697 = STE-U 8397 = CSN273* KY906709 KY906708 CBS 142698 = STE-U 8396 = PMM2445 KY906943 KY906942 CBS 109479* AY579330 AY579267 CBS 110118 AY579324 AY579261 P. junior P. krajdenii 123 Author's personal copy Fungal Diversity (2019) 94:41–129 85 Table 11 (continued) Species Isolate TUB2 Actin P. longicollarum CBS 142699 = STE-U 8393 = CSN84* KY906689 KY906688 CBS 142700 = STE-U 8395 = PMM1900 KY906879 KY906878 STE-U 8394 = CSN655 KY906733 KY906732 P. luteum CBS 137497 = A16* KF823800 KF835406 P. meliae CBS 142709 = STE-U 8391 = CSN256 KY906705 KY906704 CBS 142710 = STE-U 8392 = PMM975* KY906825 KY906824 CBS 110156* DQ173110 DQ173139 CBS 110157 DQ173111 DQ173140 P. occidentale ICMP 17037* EU596524 EU595460 P. oleae CBS 142701 = STE-U 8381 = CSN403 KY906719 KY906718 CBS 142704 = STE-U 8385 = PMM2440* KY906937 KY906936 P. pallidum CBS 120862 = STE-U 6104* EU128103 EU128144 P. parasiticum CBS 860.73* AF246803 AY579253 CBS 514.82 AY579306 AY579240 P. paululum CBS 142705 = STE-U 8389 = PMM1914* KY906881 KY906880 Phaeoacremonium pravum CBS 142686 = STE-U 8363 = CSN3* KY084246 KY084248 CBS 142687 = STE-U 8364 = CSN11 KY084245 KY084247 P. novae-zealandiae Phaeoacremonium proliferatum P. prunicola CBS 142706 = STE-U 8368 = PMM2231* KY906903 KY906902 CBS 142707 = STE-U 8369 = PMM990 KY906827 KY906826 STE-U 5967, CBS 120858, Ex-type EU128095 EU128137 STE-U 5968 EU128096 EU128138 P. pseudopanacis CPC 28694 = CBS 142101* KY173609 KY173569 P. roseum PARC273* KF764658 KF764506 P. rosicola CBS 142708 = STE-U 8390 = PMM1002* KY906831 KY906830 P. rubrigenum CBS 498.94* AF246802 AY579238 CBS 112046 AY579305 AY579239 P. santali CBS 137498 = A28* KF823797 KF835403 P. scolyti CBS 112585, CCF 3266 AY579292 AY579223 CBS 113597, STE-U 3092* AF246800 AY579224 P. sicilianum CBS 123034 = 48Pal* EU863488 EU863520 CBS 123035 = 49Pal EU863489 EU863521 P. spadicum CBS 142711 = STE-U 8386 = PMM1315* KY906839 KY906838 CBS 142714 = STE-U 8388 = CSN49 KY906667 KY906666 P. sphinctrophorum CBS 337.90* DQ173113 DQ173142 CBS 694.88 DQ173114 DQ173143 CBS 113584* AY579298 AY579231 CBS 113587 AY579299 AY579232 P. tardicrescens CBS 110573* AY579300 AY579233 P. tectonae MFLUCC 13-0707* KT285563 KT285555 P. theobromatis CBS 111586* DQ173106 DQ173132 P. subulatum P. tuscanicum CBS 123033 = 1Pal* EU863458 EU863490 P. venezuelense CBS 651.85* AY579320 AY579256 CBS 113595 AY579319 AY579255 P. vibratile CBS 117115 DQ649063 DQ649064 P. viticola CBS 101738 = LCP 93 3886* AF192391 DQ173131 CBS 113065 DQ173105 DQ173128 Pleurostomophora richardsiae CBS 270.33* AY579334 AY579271 Wuestineaia molokaiensis CBS 114877 = STE-U3797* AY579335 AY579272 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher stains are in bold 123 Author's personal copy 86 123 Fungal Diversity (2019) 94:41–129 Author's personal copy Fungal Diversity (2019) 94:41–129 b Fig. 11 Phylogenetic tree generated by maximum likelihood analysis of combined TUB2 and ACT sequence data of Phaeoacremonium species. Sequences were obtained from GenBank. Ninety-seven strains are included in the analyses, which comprise 815 characters including gaps. Single gene analyses were carried out to compare the topology of the tree and clade stability. Tree was rooted with Wuestneia molokaiensis (CBS 114877) and Pleurostomophora richardsiae (CBS 270.33). Tree topology of the Bayesian analysis was similar to the RAxML. The best scoring RAxML tree with a final likelihood value of - 14544.681166 is presented. The matrix had 591 distinct alignment patterns, with 4.52% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.225480, C = 0.307476, G = 0.225692, T = 0.241352; substitution rates AC = 1.148614, AG = 4.470582, AT = 1.079312, CG = 0.984112, CT = 4.144633, GT = 1.000000; gamma distribution shape parameter a = 1.818569. RAxML support values greater than 50% (left), Bayesian posterior probabilities greater than 0.90 (middle) and MP bootstrap value higher than 50% (right) are indicated near the nodes. The scale bar indicates 0.08 changes per site. The ex-type strains are in bold hymenophore is poroid, with pores irregularly rounded, fulvous brown to deep brown. The hyphal system is dimitic with skeletal hyphae restricted to the trama of tube layer: in the context, generative hyphae thin- to thick-walled, first regularly septate, branched, becoming sclerified and some portions of thick-walled hyphae sparsely simple-septate, and in the trama, simple septate generative and skeletal hyphae. Setae and other sterile elements are absent. The basidiospores are broadly ellipsoid to ellipsoid, adaxially flattened, smooth, thick-walled and yellow in lactophenol, becoming chestnut brown in KOH solution, weakly cyanophilous, IKI- (Drechsler-Santos et al. 2016). Phellinotus neoaridus is very common on Caesalpinia sp., while Ph. piptadeniae on Piptadeniae spp., with reports also on Libidibia glabrata, Mimosa sp., Pithecellobium excelsum, Senegalia sp. and Eugenia rostrifolia (Salvador-Montoya et al. 2015; Drechsler-Santos et al. 2016). Classification—Agaricomycetes, incertae sedis, Hymenochaetales, Hymenochataceae Type species—Phellinotus neoaridus Drechsler-Santos et al., in Drechsler-Santos et al., Phytotaxa 261(3): 222 (2016) Distribution—Brazil, Peru Disease Symptoms—No evident symptoms in the tree, but when the basidioma is removed, rot is visible; when stems or branches are cut, a black line delimiting a less dense zone in the wood is visible both in the cortex and core. Teixeira (1950) reported defoliation, progressive die-back of twigs and branches, and discoloration of the heartwood of Piptadenia communis older than 8-10 years. Hosts—mostly on living Fabaceae (Caesalpinia sp., Libidibia glabrata, Mimosa sp., Piptadenia sp., Pithecellobium excelsum, Senegalia sp.), and one report on Myrtaceae (Eugenia rostrifolia). 87 Table 12 Phellinotus. Details of the isolates used in the phylogenetic analyses Species Voucher LSU ITS P. neoaridus URM80764 KM211287 – P. neoaridus PH5 MG806098 – P. neoaridus URM80362* KM211286 KM211294 P. neoaridus URM82501/ BDNA1044 MH048088 – P. neoaridus URM84716/BDNA99 MH048090 – P. neoaridus URM85669/BDNA92 MH048089 – P. piptadeniae MF044 KP412282 KP412305 P. piptadeniae MF038 KP412278 KP412299 P. piptadeniae URM80361 KM211280 KM211288 P. piptadeniae URM80345 KM211283 KM211291 P. piptadeniae URM80322 KM211282 KM211290 P. piptadeniae URM80768 KM211281 KM211289 Ex-type (ex-epitype) strains are in bold and marked with an * Morphological based identification and diversity The two species of Phellinotus were previously identified as Phellinus rimosus (Berk.) Pilát (= Phellinotus neoaridus) and Phellinus piptadeniae Teixeira (= Phellinotus piptadeniae) (Teixeira 1950; DrechslerSantos et al. 2010). However, after molecular analyses followed by detailed morphological studies, they were accommodated in the new genus Phellinotus and one new species was described (Drechsler-Santos et al. 2016). The geographical distribution of the species is of interest as the type specimen of Phellinus rimosus was from Australia (Tasmania), thus specimens collected elsewhere and identified as such should be re-examined and new species may be discovered. This genus can be identified by the morphology of its basidiomata and by the occurrence mostly on living Fabaceae. Molecular based identification and diversity The taxonomy of Phellinotus was recently determined based on a combined dataset of ITS and LSU rDNA sequence data (Drechsler-Santos et al. 2016) of species previously identified as Phellinus rimosus and Phellinus piptadeniae. However, they nested in Fomitiporella (Dai, pers. com.; Crous et al. 2018) and the use of more markers is desirable for a better understanding of their status. Here we present an updated phylogeny for Phellinotus (Table 12, Fig. 12) based on the combined analyses of ITS and LSU rDNA sequence data. This tree includes the sequence of the type species of the genus and new sequences of P. neoaridus. Recommended genetic marker (Genus level)—LSU 123 Author's personal copy 88 Fungal Diversity (2019) 94:41–129 Fig. 12 Phylogenetic tree generated by Bayesian inference (BI) of combined ITS and LSU rDNA sequence data of Phellinotus species. Thirteen samples are included in the analyses, which comprise 1491 characters including gaps. Tree was rooted with Hymenochaete rubiginosa (He1049). Tree topology of the BI was similar to the maximum likelihood (ML) analysis. The matrix had 633 phylogenetic informative sites (42, 45%). Estimated base frequencies were as follows; A = 0.233, C = 0.222, G = 0.308, T = 0.237; substitution rates AC = 1.000, AG = 1.867, AT = 1.000, CG = 1.000, CT = 1.867, GT = 1.000; gamma distribution shape parameter a = 0.560. Bayesian posterior probabilities and ML bootstrap values C 50% are shown respectively near the nodes. The scale bar indicates 0.1 changes per site. Sequences generated in this study and of the types are in bold Recommended genetic markers (Species level) –ITS, TEF1-a and RPB2 as additional markers lost during World War II (Ariyawansa et al. 2015a) and therefore later Boerema and Van Kesteren (1964) replaced the type species of Plenodomus by Pl. lingam (sexual morph: Leptosphaeria maculans). Plenodomus species are widely distributed throughout the world with species mainly causing cankers and leaf spots associated with a wide variety of substrates (Wijayawardene et al. 2017b; Farr and Rossman 2019). Plenodomus includes several well known important plant pathogens, such as Pl. biglobosus, Pl. lindquistii, Pl. tracheiphilus, and Pl. wasabiae (Marin-Felix et al. 2017). Most of the pathogenic records are for Plenodomus destruens and molecular BLAST results in GenBank show that this species belongs to Valsaceae in Sordariomycetes. Therefore, the pathogenetic virulence of this genus requires further investigation with more taxon sampling and DNA based sequence analyses. Accepted number of species: Two species References: Teixeira (1950) (morphology), DrechslerSantos et al. (2010), Salvador-Montoya et al. (2015) (ecology, morphology), Drechsler-Santos et al. (2016) (morphology, phylogeny). Plenodomus Preuss, Linnaea 24:145 (1851) For synonyms see Index Fungorum (2019) Background The genus Plenodomus is one of the oldest pleosporalean genera with a long history of taxonomic debate. Preuss (1851) introduced Plenodomus based on Pl. rabenhorstii (de Gruyter et al. 2013, Ariyawansa et al. 2015a). However, the type material of Pl. rabenhorstii was 123 Author's personal copy Fungal Diversity (2019) 94:41–129 Table 13 Plenodomus. Details of the isolates used in the phylogenetic analyses 89 Species Isolate ITS RPB2 TUB2 Leptosphaeria doliolum CBS 505.75 JF740205 KY064035 JF740144 L. etheridgei CBS 145.84 JF740254 Plenodomus agnitus CBS 121.89 JF740194 KY064036 KY064053 P. biglobosus CBS 119951 JF740198 KY064037 KY064054 P. chrysanthemi CBS 539.63* JF740253 KY064038 KY064055 P. collinsoniae CBS 120227 JF740200 KY064039 KY064056 P. confertus CBS 375.64 AF439459 KY064040 KY064057 P. congestus CBS 244.64 AF439460 KY064041 KY064058 P. deqinensis CGMCC 3.18221 KY064027 KY064034 KY064052 P. enteroleucus CBS 142.84* JF740214 KY064042 KT266266 P. fallaciosus CBS 414.62 JF740222 KY064043 P. guttulatus MFLUCC 15-1876 KT454721 P. hendersoniae CBS 113702 JF740225 JF740160 KY064044 KT266271 P. influorescens CBS 143.84* JF740228 KY064045 KT266267 P. libanotidis P. lindquistii CBS 113795 CBS 381.67 JF740231 JF740233 KY064046 KY064059 P. lingam CBS 260.94 JF740235 KY064047 KY064060 P. lupine CBS 248.92 JF740236 KY064048 P. pimpinellae CBS 101637* JF740240 KY064061 KY064062 P. sinensis MFLU 17-0767* MF072721 P. sinensis MFLU 17-0757P* MF072722 P. salvia MFLUCC 130219 KT454725 P. tracheiphilus CBS 551.93 JF740249 KY064049 KT266269 P. viscid CBS 122783* JF740256 KY064050 KY064063 P. wasabiae CBS 120119 JF740257 KT266272 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher stains are in bold There are few sexual records for this genus and recently Tennakoon et al. (2017) introduced Plenodomus sinensis as a sexual morph with an updated molecular phylogeny in this genus. Classification—Dothideomycetes, Pleosporomycetidae, Pleosporales, Leptosphaeriaceae Type species—Plenodomus lingam (Tode: Fr.) Höhn., Sber. Akad. Wiss.Wien, Math.-naturw. Kl., Abt. 1 120:463 (1911) Distribution—Worldwide Disease Symptoms—Foot rot, Die back, Mal secco of Citrus, wilting Symptoms may vary according to the host. The typical symptoms consists of red discoloration strands in the xylem of stems, veinal chlorosis, wilt and shedding of leaves resulting in ultimate dieback of twigs and branches (Nachmias et al. 1979; Migheli et al. 2009). In seedbeds, seedlings become yellow, especially the lower leaves resulting in wilt and death of the plant. In the field, plants show a blackening of the tree around the soil level extending upward and downward. The lower part rots, and root system disintegrates. Affected stems may girdle and death of plant will follow (Lopes and Silva 1993). Hosts—Plenodomus species are recorded from at least 50 plant genera in Apiaceae, Arecaceae, Bignoniaceae, Brassicaceae, Convolvulaceae, Cucurbitaceae, Fabaceae, Gesneriaceae, Lamiaceae, Liliaceae, Moraceae, Oleaceae, Pandanaceae, Poaceae, Ranunculaceae, Rosaceae, Rutaceae, Salicaceae, Santalaceae, Urticaceae and Vitaceae as either saprobes or pathogens (Farr and Rossman 2019). Morphological based identification and diversity Plenodomus species are characterized by the ability of their asexual morph to produce scleroplectenchyma in the peridium of the pycnidium, i.e. hyaline cells with thick walls and a relatively small lumen (Boerema et al. 1994). The sexual morph is characterized by papillate, ostiolate ascomata, scleroplectenchymatous cells in the peridium, short pedicellate, cylindrical asci, and cylindrical to ellipsoidal, multi-septate pigmented ascospores (Ariyawansa et al. 2015a). Nevertheless, the simple generic diagnosis such as ‘scleroplectenchyma-producing’ defined by Boerema et al. (1994) which is similar to some species of other 123 Author's personal copy 90 Fungal Diversity (2019) 94:41–129 Fig. 13 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, TUB2 and RPB2 sequence data of Plenodomus species. Related sequences were obtained from GenBank. Twentyfive strains are included in the analyses, which comprise 1695 characters including gaps. Tree was rooted with Leptosphaeria doliolum (CBS 505.75) and L. etheridgei (CBS 145.84). The best scoring RAxML tree with a final likelihood value of - 10464.446766 is presented. The matrix had 651 distinct alignment patterns, with 23.12% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.228545, C = 0.263966, G = 0.25175, T = 0.25574; substitution rates AC = 1.629051, AG = 5.903589, AT = 1.764611, CG = 1.424439, CT = 9.08177, GT = 1.000000; gamma distribution shape parameter a = 0.359918. RAxML bootstrap support values C 60% (BT) are shown respectively near the nodes. The scale bar indicates 0.07 changes per site. T, ET and PT indicate ex-type, ex-epitype, and ex-paratype strains, respectively genera e.g. Leptosphaeria, has made Plenodomus a large, heterogeneous assemblage and Index Fungorum currently lists 97 epithets. The exact familial placement of these epithets are obscure due to lack of molecular data (\ 25 taxa have DNA data out of those 97 epithets) and it is necessary to recollect these taxa from type localities, isolate them in axenic culture, and analyse their DNA sequence data to integrate them into appropriate taxonomic ranks. Wijayawardene et al. (2017b) estimated there were 18 species in this genus. Most recently, Marin-Felix et al. (2017) accepted 20 species in their molecular phylogenetic analyses. Species delimitation in Plenodomus based on morphology is difficult due to the overlapping of morphological characters among many species (de Gruyter et al. 2013). Therefore, DNA sequence data is very important in species identification within this genus. Molecular based identification and diversity To achieve better generic and species delimitation, phylogenetic studies using ITS, TUB2 and RPB2 were recently performed (Marin-Felix et al. 2017). Phylogenetic studies based on these loci made it possible to reallocate species of Plenodomus to their exact genera (de Gruyter et al. 2013). We update the phylogeny of this genus based on a combined ITS, TUB2 and RPB2 sequence data obtained from available cultures including ex-type, exepitype and ex-paratype strains (Table 13, Fig. 13). Topological structure obtained in this study is in accordance with Marin-Felix et al. (2017) and Tennakoon et al. (2017). 123 Recommended genetic marker (Genus level)—LSU Recommended genetic markers (Species level)—ITS, TUB2 and RPB2 Author's personal copy Fungal Diversity (2019) 94:41–129 Based on our phylogeny, we observed that TUB2 gives a high resolution compared to other gene regions, such that it can be readily used to determine the placement of Plenodomus species. It is recommended to use a combination of ITS, TUB2 and RPB2 sequence data for a better resolution. Accepted number of species: There are 97 species epithets in Index Fungorum (2019) under this genus. However, 22 are accepted. References: de Gruyter et al. (2013), Ariyawansa et al. (2015a), Marin-Felix et al. (2017), Tennakoon et al. (2017) (morphology, phylogeny). Pseudopyricularia Klaubauf, M.-H. Lebrun & Crous, in Klaubauf et al., Stud. Mycol. 79: 109 (2014) Background Pseudopyricularia is a dematiaceous hyphomycete genus introduced by Klaubauf et al. (2014) based on the type species P. kyllingae Klaubauf, Lebrun & Crous. The genus name refers to its morphological similarity to Pyricularia. Pseudopyricularia species are plant pathogens mostly associated with sedges, but they can also occur on other plants. Pseudopyricularia taxa have been also recorded as saprobes, e.g. P. higginsii was found saprobic on dead leaves of Typha orientalis (Typhaceae) (Klaubauf et al. 2014). Classification—Sordariomycetes, Diaporthomycetidae, Magnaporthales, Pyriculariaceae Type species—Pseudopyricularia kyllingae Klaubauf, M.H. Lebrun & Crous, in Klaubaufet al., Stud. Mycol. 79: 109 (2014) Distribution—Iran, Israel, Japan, New Zealand and Philippines Disease Symptoms—Leaf spot The symptoms start as minute scattered angular, water soaked translucent spots on lower surface of leaves, which enlarge and appear on upper surface. Hosts—Main pathogens on Cyperaceae (Klaubauf et al. 2014). Pseudopyricularia bothriochloae was found on Bothriochloa bladhii (Poaceae) causing angular leaf spots (Marin-Felix et al. 2017), and P. iraniana can infect leaves of Juncus sp. (Pordel et al. 2017). Morphological based identification and diversity Pseudopyricularia species are characterized by solitary conidiophores with mostly terminal conidiogenous cells that form a rachis with several protruding, flat-tipped denticles, and obclavate, brown, guttulate, septate conidia with a truncate, slightly protruding, not darkened hilum (Klaubauf et al. 2014). Ellis (1976) considered Pyricularia higginsii (presently referred to as Pseudopyricularia higginsii) as a synonym under Dactylaria. However, it was not accepted by subsequent studies (Bussaban et al. 2005; 91 Klaubauf et al. 2014). Some Pseudopyricularia species were formerly described in Pyricularia. Several isolates previously recognized as Pyricularia higginsii were later confirmed as a species complex which represents three related species (P. cyperi, P. kyllingae, P. higginsii) belonging to Pseudopyricularia (Klaubauf et al. 2014). Pyricularia bothriochloae was also transferred to Pseudopyricularia bothriochloae (Marin-Felix et al. 2017). Species of Pseudopyricularia can be mainly differentiated from Pyricularia sensu stricto by having short, determinate, brown conidiophores with an apical rachis with flattipped denticles. However, because of the similarity of conidial characters, morphological species identification of Pseudopyricularia is challenging. Conidial characters cannot be used alone as taxonomic criterion at generic level without phylogenetic analyses (Klaubauf et al. 2014). Molecular based identification and diversity DNA sequence data is crucial for species identification in Pseudopyricularia and morphology similar taxa. Previous studies were mainly based on morphological identification. The order Magnaporthales previously comprised the monotypic family Magnaporthaceae which contains 13 genera and more than 100 species (Zhang et al. 2011a, b; Illana et al. 2013; Luo and Zhang 2013; Klaubauf et al. 2014). Klaubauf et al. (2014) carried out phylogenetic analyses on Pyricularia species based on combined ITS, LSU, RPB1, ACT, CAL sequence data. The result revealed two new families, namely Ophioceraceae and Pyriculariaceae, and ten new genera, including Pseudopyricularia; three species were included in Pseudopyricularia. Crous et al. (2015) described the fourth species Ps. hagahagae Crous & M.J. Wingf. based on LSU sequence data. MarinFelix et al. (2017) found that P. bothriochloae was located in the Pseudopyricularia clade in a phylogenetic tree based on ITS and LSU sequence data, thus P. bothriochloae was combined under Ps. bothriochloae. The latest phylogenetic study on Pseudopyricularia was carried out by Pordel et al. (2017). LSU and RPB1 sequence data revealed two new Pseudopyricularia species, P. hyrcaniana A. Pordel & M. Javan-Nikkhah and Ps. iraniana A. Pordel & M. JavanNikkhah. The present study reconstructs the phylogeny based on analyses of ITS, LSU, RPB1, ACT and CAL sequence data for this genus, with all the species accepted to date, and it corresponds to previous studies (Pordel et al. 2017) (Table 14, Fig. 14). Recommended genetic markers (Genus level)—LSU, RPB1 Recommended genetic markers (Species level)—ACT, RPB1, ITS, CAL Accepted number of species: Seven species References: Klaubauf et al. (2014), Pordel et al. (2017) (morphology, phylogeny). 123 Author's personal copy 92 Fungal Diversity (2019) 94:41–129 Table 14 Pseudopyricularia. Details of the isolates used in the phylogenetic analyses Species Isolate ITS LSU RPB1 ACT CAL Macgarvieomyces borealis CBS 461.65* KM484854 DQ341511 KM485070 KM485170 KM485239 M. juncicola CBS 610.82 KM484855 KM484970 KM485071 KM485171 KM485240 Pseudopyricularia bothriochloae CBS 136427* KF777186 KY905701 KY905700 P. cyperi CBS 133595* KM484872 KM484990 AB818013 AB274453 AB274485 P. cyperi CBS 665.79 KM484873 DQ341512 KM485093 KM485178 KM485248 P. cyperi PH0053 KM484874 KM485094 KM485179 KM485249 P. hagahagae CPC 25635* KT950851 KT950877 KT950873 P. higginsii CBS 121934 KM484875 KM484991 KM485095 KM485180 P. hyrcaniana IRAN2758C* KP144447 KP144452 KY457270 P. hyrcaniana UTFC-PO11 KP144448 KY457266 KY457271 KY457261 P. hyrcaniana P. iraniana UTFC-PO12 IRAN 2761C* KM207211 KY457258 KY457267 KY457268 KY457272 KY457273 KY457262 KY457264 P. iraniana UTFC-PO12 KM207210 KP144454 P. kyllingae CBS 133597* KM484876 KM484992 KM485096 AB274451 AB274484 P. kyllingae PH0054 KM484877 KM484993 KM485097 KM485181 KM485251 KM485250 KY457260 KY457263 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold Tilletia Tul. & C. Tul., Annls Sci. Nat., Bot., sér. 3 7: 112 (1847) Background Tulasne and Tulasne (1847) named Tilletia (Tilletiaceae, Exobasidiales) after Matthieu du Tillet (1714–1791), who first determined the pathogenicity of T. caries on wheat in France (Vánky and Shivas 2008). Tillet showed that washed seed reduced the spread of smut, although he was unaware the disease was caused by a fungus (Carefoot and Sprott 1967). Species of Tilletia cause smut in the inflorescences and leaves of grasses (Poaceae). They are either localized in individual ovaries or systemic in the inflorescence. The species of Tilletia on cultivated grasses can cause economic losses and have been intensively studied. For example, several species, including T. caries, replace the grains of wheat with masses of spores that produce trimethylamine, which has an odour of rotten fish. Consequently, ginger-bread was invented as a solution to mask the smell of smutted grain (Carefoot and Sprott 1967). Tilletia indica is a billion dollar threat to the wheat industries in Australia and the USA (Murray and Brennan 1998; Rossman 2009). The misidentification of T. indica in grain from both of these countries has been discussed (Castlebury and Carris 1999; Pascoe et al. 2005). Castlebury et al. (2005) determined that association of spore morphology, germination patterns and relationships with hosts were unclear in some clades of Tilletia. Systemic species of Tilletia germinate to form basidiospores that conjugate while attached to the basidium, and form dikaryotic hyphae that infect host seedlings. Localized 123 species of Tilletia form basidiospores that do not conjugate on germination from the basidium (Castlebury et al. 2005). The systemic species usually have reticulate spores, whereas the localized species have verrucose spores (Castlebury et al. 2005). Classification—Exobasidiomycetes, Exobasidiomycetidae, Tilletiales, Tilletiaceae Type species—Tilletia caries (DC.) Tul. & C. Tul., Annls Sci. Nat., Bot., sér. 3 7: 113 (1847) Distribution—Worldwide Disease Symptoms—Sori mostly replace ovaries of infected grasses with a mass of powdery black or brown spores. The ovaries are often hypertrophied and the infection can be systemic or localised. Sori are sometimes produced on the leaves and culms of infected plants. Hosts—Poaceae Morphological based identification and diversity Vánky (2011) listed 178 taxa in his world monograph of smut fungi. Since then only three further species, T. geeringii, T. mactaggartii and T. marjaniae, have been described, all from Australia on species of Eriachne (Li et al. 2014). Castlebury et al. (2005) found that Conidiosporomyces, Ingoldiomyces and Neovossia, collectively represented by only five species, were congeneric with Tilletia. Chandra and Huff (2008) established the monotypic Salmacisia, which was sister to Tilletia. Salmacisia buchloeana grouped with Tilletia, sister to T. dactyloctenii, in the present analysis. Vánky (2011) used host taxonomy as the most important character to identify species of Tilletia. The size and ornamentation of spores is used to further identify species on the same host genera (see http:// Author's personal copy Fungal Diversity (2019) 94:41–129 93 Fig. 14 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, LSU, RPB1, ACT and CAL sequence data of Pseudopyricularia species. Related sequences were obtained from GenBank. Fifteen strains are included in the analyses. Tree was rooted with Macgarvieomyces borealis (CBS 461.65) and M. juncicola (CBS 610.82). The best scoring RAxML tree with a final likelihood value of - 10627.314729 is presented. The matrix had 771 distinct alignment patterns, with 20.13% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.244984, C = 0.283221, G = 0.271087, T = 0.200708; substitution rates AC = 1.176383, AG = 2.920484, AT = 1.126771, CG = 1.004552, CT = 6.091634, GT = 1.000000; gamma distribution shape parameter a = 1.511342. RAxML bootstrap support values C 60% are shown respectively near the nodes. The scale bar indicates 0.02 changes per site. The ex-type (ex-epitype) strains are in bold collections.daff.qld.gov.au/web/key/smutfungi/ et al. 2014). from type specimens in the private collection of Kálmán Vánky (Herbarium Ustliaginales Vánky), which is held at the Queensland Plant Pathology Herbarium (BRIP). There are five publicly available genomes in GenBank for species of Tilletia, all of which are agriculturally important taxa. These are T. controversa, T. caries, T. walkeri (Nguyen et al. unpublished), T. horrida (Wang et al. 2015a, b) and T. indica (Sharma et al. 2016). Their genomes range in size from 20 to 37 Mb with an average size of * 28 Mb. An 18 Mb genome for Tilletia buchloeana (as Salmacisia buchloeana) was recently Shivas Molecular based identification and diversity Castlebury et al. (2005) used the large subunit (LSU) region of ribosomal DNA (rDNA) to first study species of Tilletia with a molecular approach. Single species descriptions have since been based on the internal transcribed spacer (ITS) and LSU regions (Shivas et al. 2009; McTaggart and Shivas 2009; Li et al. 2014). The present study builds on work by previous authors and provides molecular barcodes for the ITS and LSU regions sequenced 123 Author's personal copy 94 released (Huff et al. 2017). An ongoing challenge for genomic studies of Tilletia is that these taxa are difficult to grow in culture, which limits the amount of DNA available for genomic analysis. This study reconstruct the phylogeny of Tilletia based on analyses of combined ITS and LSU sequence data. The molecular barcodes of rDNA gene regions provided from type specimens in the present study will aid identification of known taxa. However, for further resolution within Tilletia, additional markers will be required. There was no phylogenetic support for the larger clades in the current analyses (Fig. 15). Recommended genetic marker (Genus level)—LSU Recommended genetic marker (Species level)—ITS Accepted number of species: There are 336 species epithets in Index Fungorum (2019) under this genus, of which 181 are in use. References: Castlebury et al. (2005), Shivas et al. (2009, 2014), McTaggart and Shivas (2009), Vánky (2011), Li et al. (2014) (morpholy and phyogeny); Wang et al. (2015a, b), Sharma et al. (2016), Huff et al. (2017) (genome). Venturia Sacc., Syll. fung. (Abellini) 1: 586 (1882) Background The genus Venturia was introduced by Saccardo (1882), for V. inaequalis (Cooke) G. Winter. Most of the species in this genus are notable plant pathogens, e.g. apple scab (V. inaequalis), pear scab (V. pyrina Aderh.), poplar shoot blight (V. populina (Vuill.) Fabric.), and stone fruit scab or freckle (V. carpophil E.E. Fisher). The taxonomic concept of Venturia was adopted by Sivanesan (1977). Molecular evidence indicated that Venturia is a genus within Venturiales, Dothideomycetes (Zhang et al. 2011a, b; Hyde et al. 2013). Classification—Dothideomycetes, Pleosporomycetidae, Venturiales, Venturiaceae Type species—Venturia inaequalis (Cooke) G. Winter, in Thümen, Mycoth. Univ., cent. 3: no. 261 (1875) Distribution—Worldwide Disease Symptoms—Leaf blight/spot, Scab Symptoms are more noticeable on leaves and fruits. Nearly circular, velvety, olive-green spots on both sides of the leaves appear in early spring. The spots eventually turn dark green to brown and the leaves will turn yellow and fall. Lesions on the leaves and fruit are ‘‘scabby’’ in appearance, with a distinct margin. The earliest noticeable symptom on fruit is water-soaked areas which develop into velvety, green to olive-brown lesions (Vaillancourt and Hartman 2000). 123 Fungal Diversity (2019) 94:41–129 Fig. 15 Phylogram of 89 species of Tilletia obtained from a c maximum likelihood search (command –f a) of concatenated ITS and LSU gene regions in RAxML v. 8.2 (Stamatakis 2014). Bootstrap values (C 70%) from 1000 maximum likelihood replicates above nodes and posterior probability values (C 0.95) summarized from 30,000 converged trees in a Bayesian search below nodes. Taxa sequenced from a type specimen in bold font. The tree was rooted to Erratomyces patellii and all GenBank numbers are provided in Table 15 Hosts—broad host range including genera Acer, Achilea, Alchemilla, Allium, Alnus, Betula, Epilobium, Malus, Pandanus, Persea, Pinus, Populus, Prunus, Quercus and Salix (Farr and Rossman 2019). Morphological based identification and diversity Species of Venturia are parasitic or endophytic on leaves, bark and wood, immersed and becoming erumpent, black, globose ascomata, with papillate, ostiolate, bitunicate, oblong to obclavate asci, with or without short and thick pedicel, with an ocular chamber, uniseriate, ellipsoidal, broadly rounded ends, hyaline to pale brown, 1-septate ascospores, with upper cell shorter than the lower one (Wu et al. 2011; Hyde et al. 2013). The asexual morph of this genus was found as two genera, Pollaccia E. Bald. & Cif. and Spilocaea Fr. (Barr 1968; Sivanesan 1984; Crous et al. 2007). Seifert and Gams (2011) synonymized Spilocaea under Fusicladium Bonord., however, Zhang et al. (2011a, b) indicated that the type species of Spilocaea (S. pomi Fr.) is the asexual morph of Venturia based on molecular analyses. Therefore, Spilocaea was synonymized under Venturia based on the number of its epithets being higher than Spilocaea (Index Fungorum 2019). Currently, about 180 species are listed in Index Fungorum (2019), but many of them lack clear description and illustration. There are little sequence data for Venturia available in GenBank when compared with the number of species listed in Index Fungorum (2019). Fresh collections and molecular data are needed to clarify relationships between species (Zhang et al. 2011a, b; Hyde et al. 2013). The species are distinguished by hosts, disease symptoms, morphology of ascomata, number of ascospores in the ascus, and shape and colour of ascospores. However, most species have unclear descriptions. Thus, it is difficult to compare unknown/newly collected Venturia species with described species. Molecular analysis is an important method for identifying species in Venturia, but not many species have such data. Molecular based identification and diversity Sequence data has been provided from both sexual and asexual morphs (Crous et al. 2007; Zhang et al. 2011a, b). Author's personal copy Fungal Diversity (2019) 94:41–129 95 123 Author's personal copy 96 In phylogenetic trees, Venturia was placed in a monophyletic clade of Venturiaceae, which is a sister group to Symphoventuriaceae (Zhang et al. 2011a, b; Hyde et al. 2013). It is closely related to Microthyriales with Phaeotrichaceae as a sister clade (Schoch et al. 2009; Wu et al. 2011; Hyde et al. 2013, Liu et al. 2017). We update the phylogenetic relationship of Venturia species by analysing concatenated alignment of SSU, LSU and ITS sequence data (Table 16, Fig. 16). Based on this phylogenetic tree, the placement of species within this genus are not different from previous studies. Only a few species are confidently identified and established due to little sequence data from Venturia species available in GenBank. Recommended genetic markers (Genus level)—LSU, SSU Recommended genetic marker (Species level)—ITS Accepted number of species: There are 276 species epithets in Index Fungorum (2019) under this genus. However, around 20 species are confirmed by sequence data (Hyde et al. 2013; Zhang et al. 2016). References: Crous et al. (2007), Zhang et al. (2011a, b) (morphology, phylogeny), Carisse et al. (2010) (life cycle and disease management), Machouart et al. (2014) (Phylogeny), Zhang et al. (2016) (Phylogeny) Waitea Warcup & P.H.B. Talbot, Trans. Br. Mycol. Soc 45(4): 503 (1962) Background The genus Waitea was founded by Warcup and Talbot (1962) for W. circinata producing small pink-orange sclerotia in soil. The resemblance of hyphae to Rhizoctonia was noted upon establishment of the genus, but at that time no described asexual morph was known. Waitea circinata was later found to be associated with the asexual Rhizoctonia zeae and shown to be a pathogen of legumes, cereals and turf grasses. Waitea circinata has a wide distribution, but is mostly tropical, and lives as a saprotroph or phytopathogen. Classification—Agaricomycetes, incertae sedis, Corticiales, Corticiaceae Type species—Waitea circinata Warcup & P.H.B. Talbot, Trans. Br. Mycol. Soc 45(4): 503 (1962) Distribution—Worldwide Disease Symptoms—Brown ring patch, Leaf and sheath blight Leaf and sheath blight or spot disease is characterized by oval lesions with green-gray centers surrounded by a distinct brown margin. Several lesions can occur together (De la Cerda et al. 2010; Kammerer et al. 2011; Chang and Lee 2016). Circular or irregular small patches of tan to yellow–brown colour are the initial symptom of brown ring patch disease and eventually develop brownish rings. Leaf 123 Fungal Diversity (2019) 94:41–129 blades turn from yellow to brown as the disease progress and die eventually (Toda et al. 2005; Ni et al. 2012). Hosts—Fabaceae (legumes) and Poaceae (cereals and turf grasses) Morphological based identification and diversity Waitea currently contains only the type species W. circinata. Waitea nuda was reduced to synonymy by Roberts (1999). The numerous available GenBank sequences of W. circinata imply that the species is frequently isolated from different parts of the world. Several varieties have been proposed for W. circinata, all shown to be nomen invalid following Articles 39.1 and 40.1 of the Melbourne Code (see Index Fungorum 2019). Molecular based identification and diversity The assignment of Waitea to Corticiaceae was already speculated by Talbot (1965), even though the genus was later frequently attributed to Ceratobasidiales based on morphology (e.g. Roberts 1999). Eventually, the phylogenetic placement of Waitea in the corticioid clade (Corticiales) was established by DePriest et al. (2005). Subsequent division of Corticiales to three families confirmed that Waitea is nested within Corticiaceae (GhobadNejhad et al. 2010). Laetisaria arvalis is a close relative of Waitea (Fig. 5). Recommended genetic marker (Genus level)—nLSU Recommended genetic marker (Species level)—ITS Amaradasa et al. (2013) showed that ITS is an effective marker to characterize the isolates of Waitea and similar agents of turf grass blights to their ‘infraspecies’ level. Accepted number of species: One species. References: DePriest et al. (2005), Ghobad-Nejhad et al. (2010), Amaradasa et al. (2013) (phylogeny), De la Cerda et al. (2010), Kammerer et al. (2011), Chang and Lee (2016) (morphology, phylogeny, pathogenicity), Ghimire et al. (2011) (morphology and phylogeny). Updates on four important phtopathogens Bipolaris Shoemaker, Can. J. Bot. 33:882(1959) For synonyms see Index Fungorum (2019) Background Species of Bipolaris are cosmopolitan and distributed throughout a broad range of environments. Bipolaris species are pathogens, saprobes or endophytes of a wide range of hosts (Hyde et al. 2014). Bipolaris oryzae critically damaged the rice cultivation in Bengal province in India and caused a devastating famine during 1943–1944 (Scheffer 1997; Hyde et al. 2014). Although not resulting in human starvation, Southern corn leaf blight caused by Author's personal copy Fungal Diversity (2019) 94:41–129 97 Table 15 Details of the isolates used in the phylogenetic analyses Taxon Voucher number ITS LSU Erratomyces patelii HUV 18697 DQ663692 AF009855 Oberwinkleria anulata HUV 16003* DQ875369 NA Salmacisia buchloëana WSP 71313 EF204936 DQ659922 Tilletia aegopogonis WSP 67743 AY818967 NA T. anthoxanthi HUV 18739* MH231773 MH231773 T. asperifolia LMC 90 NA AY818968 T. australiensis BRIP 51874 MH231774 MH231774 T. ayresii HUV 19314/BRIP 49130 AY819017 MH231775 T. barclayana Strain-832 AF310168 NA T. barclayana S-104 AF399894 NA T. barclayana T. barclayana WSP 68658 WSP 68466 NA NA AY818970 AY818971 T. bornmuelleri S 054 AF398452 NA T. boutelouae WSP 68661 NA AY818973 T. brachypodii-mexicani HUV 16007* MH231776 MH231776 T. bromi BRIP 49095 MH231777 MH231777 T. capeyorkensis BRIP 27011 MH231778 MH231778 T. caries LMC 97-136 AF398438 AY819007 T. cerebrina LMC 125 NA AY818994 T. challinoriae BRIP 52502* NR119757 NA T. chionachnes BRIP 26898* MH231779 MH231779 T. controversa V 764 AF398440 AY818995 T. dactyloctenii HUV 8887* MH231780 MH231780 T. ehrhartae BRIP 28392 MH231781 MH231781 T. elymi S 064 AF398454 NA T. eragrostiellae HUV 15805* MH231782 NA T. eremopoae T. filisora HUV 19420* BRIP 47729 MH231783 MH231784 MH231783 MH231784 T. fusca LMC 214 AF398455 AY818996 T. geeringii BRIP 51851* KF055226 NA MH231785 T. gigacellularis HUV 20555* MH231785 T. goloskokovii LMC 315 NA AY818999 T. holci V 765 AF398459 AY819008 T. horrida NA AF398435 NA T. horrida LMC 339 NA AY818974 T. horrida LMC 358 NA AY818975 T. horrid T54899 MH231786 NA T. hyalospora HUV 16038 AF133576 AF399891 T. imbecillus BRIP 7831 MH231787 MH231787 T. indica BPI 863665 AF398434 AY818977 T. iowensis BPI 863664 NA AY818988 T. ischaemi HUV17453* MH231788 MH231788 T. ixophori WSP 71170 NA AY819010 T. kimberleyensis BRIP 51857 MH231789 MH231789 T. lachnagrostidis BRIP 47300 MH231790 NA T. laevis V 766 AF398444 AY819005 T. lageniformis BRIP 47749* MH231791 MH231791 T. laguri HUV 16352* MH231792 NA 123 Author's personal copy 98 Fungal Diversity (2019) 94:41–129 Table 15 (continued) Taxon Voucher number ITS LSU T. lineata BRIP 26844* MH231793 MH231793 T. lolii S 119 AF398460 NA T. maclaganii Tm001NY09 JF745116 NA T. mactaggartii BRIP 51853* KF055227 KF055228 T. majuscule BRIP 51841* NA MH231794 T. marjaniae BRIP 49721* KF055224 KF055225 T. menieri WSP 69115 AF398456 AY819002 T. micrairae T. moliniae BRIP 52433* TUB 018922 FJ862995 EU659134 NA EU661605 T. narayanaraoana BRIP 47957 GQ497894 NA T. nigrifaciens BRIP 43865 MH231796 MH231796 T. obscura-reticulata WSP 68357 NA AY819011 T. olida BRIP 44536 MH231797 MH231797 T. opaca BRIP 27896 MH231798 MH231798 T. panici-humilis HUV 205832* MH231799 NA T. polypogonis V 931 NA AY819015 T. pseudochaetochloae BRIP 46730 MH231800 MH231800 T. pseudoraphidis BRIP 51873* MH231801 MH231801 T. pulcherrima WSP 71501 EU915293 NA MH231802 T. rostrariae HUV 14898* MH231802 T. rugispora HUV 19147/BRIP 47127 MH231803 AY818983 T. savilei V 859 AF399885 AY819018 T. sehimicola T. setariae BRIP 51847* V 934 MH231804 NA MH231804 AY819014 T. setariae-parvifolia BRIP 47735* MH231805 NA T. setariae-pumilae HUV 21399* MH231806 NA T. shivasii BRIP 52525 MH231807 MH231807 T. sporoboli HUV 1880* MH231808 NA T. sterilis LMC 363 NA AY819003 T. sumatiae HUV 17529/V933 MH231809 AY818987 T. thailandica BRIP 48134 NA MH231810 T. trabutii BRIP 46328 MH231811 MH231811 T. trachypogonis HUV 19626* MH231812 MH231812 T. triticoides S 102 AF398446 NA T. verruculosa WSP 70430 NA AY818984 T. viennotii BRIP 47077 MH231813 MH231813 T. vitatta BRIP 54207 MH231814 MH231814 T. walker BPI 746091 AF399887 AY818978 T. whiteochloae BRIP 51838 BRIP 54437 MH231815 MH231816 MH231815 MH231816 T. xerochloae Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold Bipolaris maydis in the 1970s resulted in catastrophic losses in maize crops in the USA and UK (Manamgoda et al. 2014). Bipolaris sorokiniana was confirmed as the most economically important foliar pathogen in warm areas in the conference ‘‘Wheat for the national warm areas’’ held in Brazil in 1990 (Hyde et al. 2014). Some Bipolaris species are pathogenic to humans (El-Khizzi 123 et al. 2010). Transferring agricultural commodities including plants and seeds across geographical borders without proper quarantine implementation, may have resulted in the worldwide distribution of common phytopathogenic species of Bipolaris (Manamgoda et al. 2014; Farr and Rossman 2019). Author's personal copy Fungal Diversity (2019) 94:41–129 99 Table 16 Venturia. Details of the isolates used in the phylogenetic analyses Species Isolate LSU ITS TEF Calmodulin TUB SSU Fusicladium peltigericola CBS:128206 HQ599579 HQ599579 – – – – Sympoventuria capensis CPC 12840 DQ885904 DQ885904 – – – – V. anemones CBS 370.55 EU035447 EU035447 KF853965 – KF808264 – V. atriseda CBS 371.55 EU035448 EU035448 – – – – V. aucupariae CBS 363.35 EU035450 EU035450 V. catenospora BJFU 140822-1 KU220966 KU220964 – – – – V. catenospora CBS 447.91 EU035427 EU035427 KF853957 – KF808256 – V. chinensis BJFU 140826-17 KP689595 KP689596 – – – – V. chlorospora CBS 470.61 EU035454 EU035454 – – – – V. chlorospora CBS 466.61 EU035453 EU035453 – – – – V. ditricha V. fraxini CBS 118894 VE4 EU035456 – EU035456 KT823548 KF853970 KT823582 – KT823616 KF808270 KT823514 – V. fuliginosa BJFU 140827.14 KU220967 KU220965 – – – – V. helvetica CBS 474.61 EU035458 EU035458 KF853974 – KF808274 – V. hystrioides CBS:117727 EU035459 EU035459 KF853975 – – – V. inaequalis CBS 309.31 EU035437 EU035437 – – – – V. inaequalis CBS 476.61 GU456336 EU282478 GU456288 – – – V. inopina MYA 2852 – AY177406 – – – – V. lonicerae CBS 445.54 EU035461 EU035461 – – – – V. macularis CBS 477.61 EU035462 EU035462 KF853977 – KF808277 – V. martianoffianum BJFC 150828_1 KU985140 KU985131 V. minuta CBS 478.61 EU035464 EU035464 KF853980 – KF808280 – V. nashicola OYO-1 – HQ434393 HQ434349 – HQ434437 – V. orni VO10 – KT823564 KT823598 KT823632 KT823530 V. phaeosepta BJFC 140520_1 KU985142 KU985133 V. pirina 38995 EF114714 HQ434425 HQ434381 – HQ434469 EF114739 V. polygoni-vivipari V. populina CBS:114207 CBS 256.38 EU035466 GU323212 EU035466 EU035467 KF853984 – – – KF808284 – – GU296206 V. saliciperda CBS 480.61 EU035471 EU035471 – – – V. tremulae CBS 112625 EU035438 EU035438 – – – V. tremulae var. tremulae CBS 257.38 EU035475 EU035475 – – – – V. viennotii CBS 690.85 EU035476 EU035476 – – – – Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold Classification—Dothideomycetes, Pleosporomycetidae, Pleosporales, Pleosporaceae Type species—Bipolaris maydis (Y.Nisik. & C. Miyake) Shoemaker, Can. J. Bot. 33:882 (1959) Distribution—Worldwide Disease Symptoms—Leaf spots, leaf blights, melting outs, common root rot, foot rot Small brown-red water soaked spots on leaves can be observed. Subsequently the disease area may turn into black/brown elliptical or fusiform lesions with gray to brown centers. On a fully developed lesion concentric rings can be observed (Lin et al. 2012; Ahmadpour et al. 2012). Decaying leaves with purple/brown lesions are observed in melting out disease (Watkins et al. 1989). Brown to black lesions on primary and secondary roots, brown discoloration of crowns, yellowing of plants and browning of sub-crown internode can be observed in common root rot disease (Arabi and Jawhar 2013). In foot rot disease, dark brown lesions on the sub-crown are caused. These lesions will eventually spread to encompass the entire sub-crown internode (Smiley and Patterson 1996). Hosts—Poaceae, including rice, maize, wheat and sorghum (Manamgoda et al. 2014). Species of Bipolaris are also recorded from at least 60 other plant genera in Anacardiaceae, Araceae, Euphorbiaceae, Fabaceae, Malvaceae, Rutaceae and Zingiberaceae as either saprobes or pathogens (Manamgoda et al. 2011; Ariyawansa et al. 2015a). 123 Author's personal copy 100 Fungal Diversity (2019) 94:41–129 Fig. 16 Phylogenetic tree generated by maximum likelihood analysis of combined ITS and LSU sequence data of Venturia species. Sequences were obtained from GenBank. Thirty two strains are included in the analyses, which comprise 1380 characters including gaps. Single gene analyses were carried out to compare the topology of the tree and clade stability. Tree was rooted with Sympoventuria capensis (CPC 12840). Tree topology of the Bayesian analysis was similar to the RAxML. The best scoring RAxML tree with a final likelihood value of - 4376.419190 is presented. The matrix had 261 distinct alignment patterns, with 15.44% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.237094, C = 0.259593, G = 0.296334, T = 0.206979; substitution rates AC = 1.996953, AG = 2.270150, AT = 1.867221, CG = 0.763559, CT = 10.363584, GT = 1.000000; gamma distribution shape parameter a = 0.419710. RAxML and Bayesian posterior probabilities values C 70% (BT) and 0.9 (PP) are shown respectively near the nodes. The scale bar indicates 0.2 changes per site. The ex-type strains are in bold Morphological based identification and diversity Correct species identification in this genus has always proven difficult, mostly relying on morphology and plant host association. Studies on morphology of the sexual morph of most Bipolaris are lacking due to difficulties to induce this morph in culture or to find it in nature 123 Author's personal copy Fungal Diversity (2019) 94:41–129 (Manamgoda et al. 2014). Manamgoda et al. (2014) revised the genus based on DNA sequence data derived from living cultures of fresh isolates, available ex-type cultures from worldwide collections and observation of type and additional specimens. They accepted 47 species in Bipolaris and clarified the taxonomy, host associations, geographic distributions and species synonymy while epi- or neotypes were designated (Ariyawansa et al. 2015a). Currently there are 131 species epithets in Index Fungorum (www.index fungorum.org; retrieved 24 March 2018). Wijayawardene et al. (2017b) estimated there were 121 species in this genus. In a recent study Marin-Felix et al. (2017) has included 40 accepted Bipolaris species to their phylogenetic analyses. To properly delineate these species, phylogenetic studies using ITS, GAPDH and TEF1-a sequences were recently performed (Manamgoda et al. 2014; Marin-Felix et al. 2017). Identification based on morphology alone is imperfect since many species have overlapping characters. The genus is morphologically similar to Curvularia and distinguishing these two genera can be problematic (Manamgoda et al. 2011, 2014). Both genera contain species with straight or curved conidia, but in Bipolaris the curvature is continuous throughout the length of the conidium, while the conidia of Curvularia have intermediate cells inordinately enlarged which contributes to their curvature (Manamgoda et al. 2011, 2014; Marin-Felix et al. 2017). Conidia in Bipolaris are usually longer than in Curvularia. Also the presence of stromata in some species of Curvularia is significant whereas this feature is not observed in Bipolaris (Manamgoda et al. 2014; Marin-Felix et al. 2017). Molecular based identification and diversity To achieve better generic and species delimitation, phylogenetic studies using ITS, GAPDH and TEF1-a were recently performed (Manamgoda et al. 2014; Hyde et al. 2014; Marin-Felix et al. 2017). Phylogenetic studies based on these loci made it possible to reallocate species of Cochliobolus (sexual morph) to either Bipolaris or Curvularia (Marin-Felix et al. 2017). We update the phylogeny of Bipolaris based on analyses of a combined ITS, GAPDH and TEF1-a sequence data (Table 17, Fig. 17) and it is in accordance with previous studies. Sequences obtained were from available ex-epitype, ex-isotype, exisolectotype, ex-paratype, ex-syntype and ex-type strains cultures. Recommended genetic marker (Genus level)—LSU Recommended genetic markers (Species level)—ITS GAPDH and TEF Accepted number of species: There are 130 species epithets in Index Fungorum (2019) under this genus. However, 40 are accepted. 101 References: Manamgoda et al. (2011, 2014), Ariyawansa et al. (2015a), Marin-Felix et al. (2017) (morphology, phylogeny). Botryosphaeria Ces. & De Not., Comm. Soc. crittog. Ital. 1(fasc. 4): 211 (1863) Background The genus Botryosphaeria (Botryosphaeriaceae) was introduced by Cesati and de Notaris (1863), revised by Saccardo (1877), and is based on the type species Botryosphaeria dothidea (Barr 1972; Slippers et al. 2004c). This genus has undergone various revisions and updates over the years, at times encompassing a diverse range of morphologies. von Arx and Müller (1954) examined 183 taxa of Botryosphaeriales and reduced them to eleven species, with extensive synonymies under B. dothidea and B. quercuum, together with nine new combinations. In later studies these synonymies were not always accepted (Shoemaker 1964; Sivanesan 1984; Slippers et al. 2004a). Slippers et al. (2004b) epitypified the type species Botryosphaeria dothidea and provided an ex-epitype culture based on morphology and phylogeny of combined ITS, TEF1-a and TUB2 sequence data. This set a firm basis for the resolution of species. Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Botryosphaeria dothidea (Moug.) Ces. & De Not., Comm. Soc. crittog. Ital. 1(fasc. 4): 212 (1863) Distribution—Worldwide Disease Symptoms—Leaf spots, cankers, dieback, fruit rot, gummosis and even plant death. Hosts—Plurivorous Morphological based identification and diversity Species in the genus Botryosphaeria have hyaline ascospores that can become pale brown with age, uniloculate ascomata often aggregated or forming botryose clusters, asexual morphs with thin-walled, aseptate, hyaline conidia that sometimes become olivaceous, occasionally forming one or two septa when aged, they typically lack a mucoid sheath and apical appendage. A search in MycoBank (July 2018) revealed 292 names in Botryosphaeria while Index Fungorum (July 2018) provided 279 names. However, only 13 species are known in culture. Dissanayake et al. (2016) included ten Botryosphaeria species in their phylogeny. Subsequently, Li et al. (2018) introduced three novel species, B. pseudoramosa, B. qingyuanensis and B. wangensis. Colony and conidial morphology are the primary characters to identify species within this genus. Colonies are olivaceous becoming grey with reverse black. Mycelial mat 123 Author's personal copy 102 Fungal Diversity (2019) 94:41–129 Table 17 Bipolaris. Details of the isolates used in the phylogenetic analyses Species Isolate ITS GAPDH TEF1-a Bipolaris austrostipae BRIP 12490* KX452442 KX452408 KX452459 B. axonopicola BRIP 11740* KX452443 KX452409 KX452460 B. bamagaensis BRIP 13577* KX452445 KX452411 KX452462 B. bicolour CPC 28811 MF490804 MF490826 MF490848 B. bicolour CPC 28825 MF490805 MF490827 MF490849 B. bicolour CBS 690.96 KJ909762 KM042893 KM093776 B. brachiariae CPC 28819* MF490806 MF490828 MF490850 B. brachiariae CPC 28820 MF490807 MF490829 MF490851 B. chloridis BRIP 10965* KJ415523 KJ415423 KJ415472 B. clavata BRIP 12530* KJ415524 KJ415422 KJ415471 B. coffeana B. cookie BRIP 14845* AR 5185 KJ415525 KJ922391 KJ415421 KM034833 KJ415470 KM093777 B. crotonis BRIP 14838 KJ415526 KJ415420 KJ415479 B. cynodontis CBS 109894 KJ909767 KM034838 KM093782 B. drechsleri CBS 136207* KF500530 KF500533 KM093760 B. gossypina BRIP 14840* KJ415528 KJ415418 KJ415467 B. heliconiae BRIP 17186* KJ415530 KJ415417 KJ415465 B. heveae CBS 241.92 KJ909763 KM034843 KM093791 B. luttrellii BRIP 14643* AF071350 AF081402 AF071350 B. maydis CPC 28823 MF490808 MF490830 MF490852 B. maydis CBS 137271* AF071325 KM034846 KM093794 B. microlaenae CBS 280.91* JN601032 JN600974 JN601017 B. microstegii CBS 132550* JX089579 JX089575 KM093756 B. oryzae CPC 28826 MF490809 MF490831 MF490853 B. oryzae CPC 28828 MF490810 MF490832 MF490854 B. oryzae MFLUCC 10-0715* JX256416 JX276430 JX266585 B. panici-miliacei B. peregianensis CBS 199.29* BRIP 12790* KJ909773 JN601034 KM042896 JN600977 KM093788 JN601022 B. pluriseptata BRIP 14839* KJ415532 KJ415414 KJ415461 B. sacchari ICMP 6227 KJ922386 KM034842 KM093785 B. saccharicola CBS 155.26* KY905674 KY905686 KY905694 B. saccharicola CBS 324.64 HE792932 KY905692 KY905699 B. saccharicola CBS 325.64 KY905675 KY905687 KY905695 B. salkadehensis Bi 1* AB675490 AB675490 AB675490 B. salviniae BRIP 16571* KJ415535 KJ415411 KJ415457 B. secalis BRIP 14453* KJ415537 KJ415409 KJ415455 B. setariae CPC 28802 MF490811 MF490833 MF490811 B. setariae CBS 141.31 EF452444 EF513206 EF452444 B. shoemaker BRIP 15929* KX452453 KX452419 KX452470 B. simmondsii BRIP 12030* KX452454 KX452420 KX452471 B. sivanesaniana BRIP 15847* KX452455 KX452421 KX452472 B. sorokiniana B. sorokiniana CPC 28832 CBS 110.14 MF490812 KJ922381 MF490834 KM034822 MF490855 KM093763 B. subramanianii BRIP 16226* KX452457 KX452423 KX452474 B. urochloae ATCC 58317 KJ922389 KM230396 KM093770 B. variabilis CBS 127716* KY905676 KY905688 KY905696 B. variabilis CBS 127736 KY905677 KY905689 KY905677 B. victoriae CBS 327.64* KJ909778 KM034811 KM093748 B. woodii BRIP 12239* KX452458 KX452424 KX452475 123 Author's personal copy Fungal Diversity (2019) 94:41–129 103 Table 17 (continued) Species Isolate ITS GAPDH TEF1-a B. yamadae CPC 28807 MF490813 MF490835 MF490856 B. yamadae CBS 202.29* KJ909779 KM034830 KM093773 B. yamadae CBS 127087 (neotype of B. euphorbiae) KY905673 KY905685 KY905693 B. zeae BRIP 11512IsoP* KJ415538 KJ415408 KJ415454 B. zeicola FIP 532* KM230398 KM034815 KM093752 Curvularia lunata CBS 730.96* JX256429 JX276441 JX266596 C. sorghina BRIP 15900* KJ415558 KJ415388 KJ415435 C. subpapendorfii CBS 656.74* KJ909777 KM061791 KM196585 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher stains are in bold is moderately dense. Conidia are narrowly fusiform, or irregularly fusiform, base subtruncate to bluntly rounded (Phillips et al. 2013). However, we consider morphological characters alone are inadequate to identify species due to plasticity and overlapping of conidial dimensions. Molecular based identification and diversity Recent advances in DNA-based molecular techniques have provided efficient tools to characterize and identify species in the genus Botryosphaeria (Slippers and Wingfield 2007; Phillips et al. 2013; Dissanayake et al. 2016; Li et al. 2018). Studies applying these tools are revealing significantly greater diversity on some hosts than was previously realized. Recent studies on the taxonomy of Botryosphaeria have employed molecular methods to reveal phylogenetic relationships among species and to resolve species complexes (Denman et al. 2003; Alves et al. 2004; Phillips et al. 2005a, b). The present phylogenetic analysis was performed based on up to date exholotype or ex-epitype sequences available in GenBank. This study updates the phylogeny of Botryosphaeria based on a combined analyses of ITS and TEF1-a sequence data (Table 18, Fig. 18) and corresponds to the previous studies. Recommended genetic markers (Genus level)—SSU, LSU Recommended genetic markers (Species level)—ITS, TEF1-a Accepted number of species: There are 282 species epithets in Index Fungorum (2019) under this genus. However, 13 are accepted. References: Phillips et al. (2013) (morphology, phylogeny), Dissanayake et al. (2016) et al. (phylogeny). Curvularia Boedijn, Bull. Jard. Bot. Buitenzorg, 3 Sér. 13: 123 (1933) For synonyms see Index Fungorum (2019) Background The cosmopolitan Curvularia consists of pathogens and saprobes of various plants, as well as opportunistic pathogens of humans and animals. They are abundantly found as the pathogens of family Poaceae (Hyde et al. 2014). Curvularia lunata, C. trifolii and C. tuberculata can cause leaf spots and leaf blights of some cereal crops such as maize, rice and horticultural crops (Bermuda grasses and turf grasses) (de Luna et al. 2002; Hyde et al. 2014). The most frequent human and animal pathogens within the genus are C. aeria, C. borreriae, C. geniculata, C. inaequalis, C. lunata and C. verrucosa (Hyde et al. 2014). Curvularia is morphologically characterized by its dark mycelium, geniculate conidiophores with sympodial, tretic conidiogenous cells, conidia with smooth to slightly verrucose wall and several false septa (distosepta) (Hyde et al. 2014). The taxonomy of Curvularia has been well studied in recent years, however the broadly perceived classification was redefined by Manamgoda et al. (2011, 2014) based on the phylogenetic relationships of ex-type strains of Curvularia species and recently collected Curvularia cultures from northern Thailand. See Hyde et al. (2014) and Marin-Felix et al. (2017) for further details. Classification—Dothideomycetes, Pleosporomycetidae, Pleosporales, Pleosporaceae Type species—Curvularia lunata (Wakker) Boedijn, Bull. Jard. bot. Buitenz, 3 Sér. 13(1): 127 (1933) Distribution—Worldwide Disease Symptoms—Leaf spots and blights, melting out, foot and root rot The first symptoms to appear on leaves are elliptical brown spots. Gradually the spots enlarge and change colour to brownish black. In melting out disease symptoms on grasses may vary depending on the extent and severity of the attack. The first symptoms are seen as small spots with purple and black specks. Melting out starts as a leaf spot which will expands to the plant base and attacks the roots and crown. Leaf wilts, necrotic roots and plant death can be 123 Author's personal copy 104 Fig. 17 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, GAPDH and TEF1-a sequence data of Bipolaris species. Related sequences were obtained from GenBank. Fifty-seven strains are included in the analyses, which comprises 1998 characters including gaps. Tree was rooted with Curvularia subpapendorfii (CBS 656.74), C. lunata (CBS 730.96) and C. sorghina (BRIP 15900). The best scoring RAxML tree with a final likelihood value of - 7757.628604 is presented. The matrix had 492 distinct alignment patterns, with 10.59% of undetermined characters or gaps. Estimated 123 Fungal Diversity (2019) 94:41–129 base frequencies were as follows; A = 0.232326, C = 0.300959, G = 0.235960, T = 0.230755; substitution rates AC = 0.597533, AG = 2.227202, AT = 0.791120, CG = 0.627286, CT = 4.571166, GT = 1.000000; gamma distribution shape parameter a = 0.779269. RAxML bootstrap support values C 60% (BT) are shown respectively near the nodes. The scale bar indicates 0.02 changes per site. T, ET IsoT IsoLT IsoPT LT , , , , and NT indicate ex-type, ex-epitype, ex-isotype, ex-isolectotype, ex-isoparatype, ex-lectotype and ex-neotype strains, respectively Author's personal copy Fungal Diversity (2019) 94:41–129 Table 18 Botryosphaeria. Details of the isolates used in the phylogenetic analyses 105 Species Isolate ITS TEF1-a LSU Botryosphaeria agaves MFLUCC 11-0125* JX646791 JX646856 JX646808 B. agaves MFLUCC 10-0051 JX646790 JX646855 JX646807 B. auasmontanum CMW 25413* KF766167 EU101348 KF766332 B. corticis CBS 119047* DQ299245 EU017539 EU673244 B. corticis ATCC 22927 DQ299247 EU673291 EU673245 B. dothidea CBS 115476* AY236949 AY236898 DQ377852 B. dothidea CBS 110302 AY259092 AY573218 EU673243 B. fabicerciana CBS 127193* HQ332197 HQ332213 N/A B. fabicerciana CMW 27108 HQ332200 HQ332216 N/A B. fusispora MFLUCC 10-0098* JX646789 JX646854 JX646806 B. fusispora MFLUCC 11-0507 JX646788 JX646853 JX646805 B. minutispermatia GZCC 16-0013* KX447675 KX447678 N/A B. minutispermatia GZCC 16-0014 KX447676 KX447679 N/A B. qingyuanensis CGMCC3.18742* KX278000 KX278105 MF410042 B. qingyuanensis B. ramosa CGMCC3.18743 CBS 122069* KX278001 EU144055 KX278106 EU144070 MF410043 N/A B. scharifii CBS 124703* JQ772020 JQ772057 N/A B. scharifii CBS 124702 JQ772019 JQ772056 N/A B. pseudoramosa CGMCC3.18739* KX277989 KX278094 MF410031 B. pseudoramosa CGMCC3.18740 KX277992 KX278097 MF410034 B. sinensia CGMCC 3.17722* KT343254 KU221233 N/A B. sinensia CGMCC 3.17724 KT343256 KU221234 N/A B. wangensis CGMCC3.18744* KX278002 KX278107 MF410044 B. wangensis CGMCC3.18745 KX278003 KX278108 MF410045 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold seen in a foot or root rot (Verma and Gupta 2010; Sunpapao et al. 2014). Hosts—Mainly found on members of Poaceae. Also occurs on Actinidaceae, Aizoaceae, Caricaceae, Convolvulaceae, Fabaceae, Iridaceae, Lamiaceae, Lythraceae, Oleaceae, Polygonaceae, Rubiaceae and Vitaceae (Farr and Rossman 2019). Morphological based identification and diversity Species of Curvularia are traditionally characterized by dark mycelium, geniculate conidiophores with sympodial, tretic conidiogenous cells and elongated conidia. The conidia are smooth to tuberculate-walled, with several false septa (distosepta) and straight or curved due to an enlarged middle cell that is often more pigmented than the other cells (da Cunha et al. 2013). However, taxonomic classification of Curvularia spp. based exclusively on morphological characteristics was insufficient for designating new species because of their phenotypic variability and this has resulted in inadequate understanding of curvularia-like species. Currently there are 156 species epithets in Index Fungorum (www.indexfungorum.org; retrieved 24 March 2018) but most of these past records lack molecular data and comprehensive morphological descriptions. In a recent study Marin-Felix et al. (2017) included 74 accepted Curvularia species to their phylogenetic analyses. Later Hyde et al. (2017) introduced Curvularia palmicola as another species and therefore, we constructed a tree with 75 Curvularia species. Species delimitation in Curvularia based on morphology only is difficult with overlapping morphological characters among many species (Manamgoda et al. 2014, 2015), as also observed in Bipolaris (see under Bipolaris). Molecular based identification and diversity To achieve proper generic and species delimitation, phylogenetic studies using ITS, GAPDH and TEF1-a sequence data were recently performed (Manamgoda et al. 2011, 2014, 2015; Hyde et al. 2014, 2017; Marin-Felix et al. 2017). Phylogenetic studies based on these loci made it possible to reallocate species of Cochliobolus (sexual morph) to either Bipolaris or Curvularia (Marin-Felix et al. 2017). We update the phylogeny of this genus based on a combined ITS GAPDH and TEF1-a sequence data obtained from available ex-epitype, ex-isotype, ex-isolectotype, ex-paratype, ex-syntype and ex-type strains cultures (Table 19, Fig. 19). Topological structure is in accordance with previous studies. 123 Author's personal copy 106 Fungal Diversity (2019) 94:41–129 Fig. 18 Phylogenetic tree generated by maximum likelihood analysis of combined ITS and TEF1-a sequence data of Botryosphaeria species. Related sequences were obtained from GenBank. Twenty five strains are included in the analyses, which comprise 903 characters including gaps. Tree was rooted with Macrophomina phaseolina (CBS 227.33). Tree topology of the ML analysis was similar to the BI. The best scoring RAxML tree with a final likelihood value of 2158.395527 is presented. The matrix had 528 distinct alignment patterns, with 17.64% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.210797, C = 0.294704, G = 0.256067, T = 0.238431; substitution rates AC = 0.448510, AG = 1.879010, AT = 0.864074, CG = 0.550809, CT = 3.948379, GT = 1.000000; gamma distribution shape parameter a = 0.387391. RAxML bootstrap support values C 50% (BT) are shown respectively near the nodes. Bayesian posterior probabilities C 0.95 (PP) indicated as thickened black branches. The scale bar indicates 0.1 changes per site. The ex-type strains are in bold Recommended genetic marker (Genus level)—LSU Recommended genetic marker (Species level)—GDPH It is recommended to use a combination of ITS GAPDH and TEF (Manamgoda et al. 2015). References: Sivanesan (1977) (morphology and pathogenicity), Manamgoda et al. (2011) (pathogenicity), Hyde et al. (2014), Marin-Felix et al. (2017) (morphology and phylogeny), Manamgoda et al. 2015 (morphology, pathogenicity and phylogeny). Neofusicoccum Crous, Slippers & A.J.L. Phillips, Stud. Mycol. 55: 247 (2006) Accepted number of species: There are 399 species epithets in Index Fungorum (2019) under this genus. However, 80 are accepted. 123 Author's personal copy Fungal Diversity (2019) 94:41–129 107 Table 19 Curvularia. Details of the isolates used in the phylogenetic tree Species Isolate ITS GAPDH TEF1-a Curvularia aeria CBS 294.61* HE861850 HF565450 C. affinis CBS 154.34* KJ909780 KM230401 C. akaii CBS 317.86 KJ909782 KM230402 KM196569 C. akaiiensis BRIP 16080* KJ415539 KJ415407 KJ415453 C. alcornii MFLUCC 10-0703* JX256420 JX276433 JX266589 C. americana UTHSC 08-3414* HE861833 HF565488 C. asiatica MFLUCC 10-0711* JX256424 JX276436 JX266593 C. australiensis BRIP 12044* KJ415540 KJ415406 KJ415452 C. australis BRIP 12521* KJ415541 KJ415405 KJ415451 C. bannonii BRIP 16732* KJ415542 KJ415404 KJ415450 C. borreriae C. bothriochloae CBS 859.73 BRIP 12522* HE861848 KJ415543 HF565455 KJ415403 KJ415449 C. brachyspora CBS 186.50 KJ922372 KM061784 KM230405 KM196588 KM196566 C. buchloes CBS 246.49* KJ909765 KM061789 C. carica-papayae CBS 135941* HG778984 HG779146 C. chiangmaiensis CPC 28829* MF490814 MF490836 C. chlamydospora UTHSC 07-2764* HG779021 HG779151 C. clavata BRIP 61680b KU552205 KU552167 KU552159 C. coicis CBS 192.29* JN192373 JN600962 JN601006 C. crustacea BRIP 13524* KJ415544 KJ415402 KJ415448 C. cymbopogonis CBS 419.78 HG778985 HG779129 HG779163 C. dactyloctenicola CPC 28810* MF490815 MF490837 MF490858 C. dactyloctenii BRIP 12846* KJ415545 KJ415401 KJ415447 C. ellisii CBS 193.62* JN192375 JN600963 JN601007 C. eragrostidis CBS 189.48 HG778986 HG779154 HG779164 C. geniculata CBS 187.50 KJ909781 KM083609 KM230410 C. gladioli C. graminicola CBS 210.79 BRIP 23186* HG778987 JN192376 HG779123 JN600964 JN601008 C. gudauskasii DAOM 165085 AF071338 C. harveyi BRIP 57412* KJ415546 KJ415400 KJ415446 C. hawaiiensis BRIP 11987* KJ415547 KJ415399 KJ415445 C. heteropogonicola BRIP 14579* KJ415548 KJ415398 KJ415444 C. heteropogonis CBS 284.91* JN192379 JN600969 JN601013 C. hominis CBS 136985* HG779011 HG779106 C. homomorpha CBS 156.60* JN192380 JN600970 JN601014 C. inaequalis CBS 102.42* KJ922375 KM061787 KM196574 C. intermedia CBS 334.64 HG778991 HG779155 HG779169 C. ischaemi CBS 630.82* JX256428 JX276440 C. kusanoi CBS 137.29 JN192381 C. lunata CBS 730.96* JX256429 JX276441 C. malina CBS 131274* JF812154 KP153179 KR493095 C. miyakei C. muehlenbeckiae CBS 197.29* CBS 144.63* KJ909770 HG779002 KM083611 HG779108 KM196568 C. neergaardii BRIP 12919* KJ415550 KJ415397 KJ415443 C. neoindica BRIP 17439 AF081449 AF081406 MF490857 JN601016 JX266596 C. nicotiae CBS 655.74* = BRIP 11983 KJ415551 KJ415396 KJ415442 C. nodosa CPC 28801 MF490817 MF490839 MF490860 C. nodosa CPC 28812 MF490818 MF490840 MF490861 123 Author's personal copy 108 Fungal Diversity (2019) 94:41–129 Table 19 (continued) Species Isolate ITS GAPDH TEF1-a C. nodosa CPC 28800* MF490816 MF490838 MF490859 C. nodulosa CBS 160.58 JN601033 JN600975 JN601019 C. oryzae CBS 169.53* KP400650 KP645344 KM196590 C. ovariicola CBS 470.90* JN192384 JN600976 JN601020 C. pallescens CBS 156.35* KJ922380 KM083606 KM196570 C. palmicola MFLUCC 14-0404* MF621582 C. papendorfii CBS 308.67* KJ909774 KM083617 KM196594 C. perotidis C. pisi CBS 350.90* CBS 190.48* JN192385 KY905678 KJ415394 KY905690 JN601021 KY905697 C. portulacae CBS 239.48* = BRIP 14541 KJ415553 KJ415393 KJ415440 C. prasadii CBS 143.64* KJ922373 KM061785 KM230408 C. protuberata CBS 376.65* KJ922376 KM083605 KM196576 C. pseudobrachyspora CPC 28808* MF490819 MF490841 MF490862 C. pseudolunata UTHSC 09-2092* HE861842 HF565459 C. pseudorobusta UTHSC 08-3458 HE861838 HF565476 C. ravenelii BRIP 13165* JN192386 JN600978 JN601024 C. richardiae BRIP 4371* KJ415555 KJ415391 KJ415438 C. robusta CBS 624.68* KJ909783 KM083613 KM196577 C. ryleyi BRIP 12554* KJ415556 KJ415390 KJ415437 C. senegalensis CBS 149.71 HG779001 HG779128 C. sesuvi Bp-Zj 01 EF175940 C. soli CBS 222.96* KY905679 KY905691 KY905698 C. sorghina C. spicifera BRIP 15900* CBS 274.52 KJ415558 JN192387 KJ415388 JN600979 KJ415435 JN601023 C. subpapendorfii CBS 656.74* KJ909777 KM061791 KM196585 C. trifolii CBS 173.55 HG779023 HG779124 C. tripogonis BRIP 12375* JN192388 JN600980 JN601025 C. tropicalis BRIP 14834* KJ415559 KJ415387 KJ415434 C. tsudae ATCC 44764* KC424596 KC747745 KC503940 C. tuberculata CBS 146.63* JX256433 JX276445 JX266599 C. uncinata CBS 221.52* HG779024 HG779134 C. variabilis CPC 28815* MF490822 MF490844 MF490865 C. variabilis CPC 28813 MF490820 MF490842 MF490863 C. variabilis CPC 28814 MF490821 MF490843 MF490864 C. variabilis CPC 28816 MF490823 MF490845 MF490866 C. verruciformis CBS 537.75 HG779026 HG779133 HG779211 C. verruculosa CBS 150.63 KP400652 KP645346 KP735695 C. verruculosa CPC 28792 MF490825 MF490847 MF490868 C. verruculosa Bipolaris maydis CPC 28809 CBS 137271* MF490824 AF071325 MF490846 KM034846 MF490867 KM093794 B. oryzae MFLUCC 10-0715* JX256416 JX276430 JX266585 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold Background When Crous et al. (2006) split Botryosphaeria into ten distinct genera they introduced Neofusicoccum for species morphologically similar to, but phylogenetically distinct from Botryosphaeria sensu lato. Despite the similar morphology, Crous et al. (2006) considered that the 123 Dichomera-like syn-asexual morph seen in some Neofusicoccum species distinguishes it from Botryosphaeria. However, the Dichomera-like syn-asexual morph has not been found in all species of Neofusicoccum and it is not produced consistently by all isolates of those species that are known to possess this state. Phillips et al. (2013) Author's personal copy Fungal Diversity (2019) 94:41–129 suggested that paraphyses, which have never been reported in conidiomata of Neofusicoccum but are known in some species of Botryosphaeria, might be a suitable character to separate the two genera. However, the similarity of paraphyses to developing conidiogenous cells makes this feature difficult to apply. Furthermore, paraphyses have not been reported in all Botryosphaeria species. Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae Type species—Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, in Crous et al., Stud. Mycol. 55: 248 (2006) Distribution—Wordwide Disease Symptoms—Dieback, Canker, Fruit rot Hosts—Plurivorous on woody hosts Morphological based identification and diversity Currently, 43 species are known in Neofusicoccum. Cultures and DNA sequence data are available for all the known species. Although Yang et al. (2017) and Li et al. (2018) included isolates of N. terminaliae in their phylogenetic analyses, no record of this species name could be found in MycoBank or Index Fungorum, but sequences are available in GenBank and a CBS culture collection number was quoted by Li et al. (2018). Since sequence data and a culture are available we provisionally include N. terminaliae as a species in Neofusicoccum. Morphologically the species are differentiated based on conidial dimensions, colouration and septation in aged conidia and pigment production in culture. Phillips et al. (2013) attempted to construct a key for identification of 22 species, but in reality plasticity of characters and overlapping of conidial dimensions rendered this attempt unreliable. Considering that a further 21 species have been introduced in Neofusicoccum since then the only reliable way to identify species is with DNA sequence data. Species cannot be identified reliably on the basis of morphological characters alone due to plasticity and overlapping of conidial dimensions. Molecular based identification and diversity Species in Neofusicoccum can be distinguished with a combination of ITS and partial TEF1-a sequences. In this way, Phillips et al. (2013) distinguished 22 species while Dissanayake et al. (2016) distinguished 29 species. However, resolution of species within some complexes is not always clearly defined and for that reason Hyde et al. (2014) recommended the use of ITS, TEF1-a and TUB2 sequence data to separate the 22 species they included in Neofusicoccum. More recently, Marin-Felix et al. (2017) used a combination of ITS, TEF1-a, TUB2 and RPB2 sequence data to resolve 34 species. Yang et al. (2017) used the same combination of loci to differentiate 31 109 named species and a further nine lineages that they declined to name. Li et al. (2018) also used a combination of ITS, TEF1-a, TUB2 and RPB2 sequence data when they introduced a further two species collected from China. Considering the recent trends we use the same combination of ITS, TEF1-a, TUB2 and RPB2 sequence data to separate 43 species in Neofusicoccum (Fig. 20). While most of the species are clearly accommodated within Neofusicoccum, N. pennatisporum and N. buxi are phylogenetically divergent and morphologically atypical of the genus. The extremely long conidia of N. pennatisporum (40–50 lm long) that can be up to 5-septate and ascospores with apical protrusions (Taylor et al. 2009) are unlike any other known species in Neofusicoccum. Conidia of N. buxi (Yang et al. 2017) are atypically shaped (sub-cylindrical) and unusually large (30–38 9 7–8 lm) for a species in Neofusioccum. Together with the divergent phylogeny these are sufficient reasons to question the inclusion of these two species in Neofusicoccum. Recommended genetic markers (Genus level)—SSU, LSU Recommended genetic markers (Species level)—ITS, TEF1-a, TUB2, RPB2 Even though it is possible to distinguish all species with a combination of ITS and TEF1-a, some species complexes are resolved more clearly with the addition of TUB2 and RPB2 sequence data. Accepted number of species: There are 41 valid species epithets in Index Fungorum (August 2018) and 41 in MycoBank (August 2018) under this genus (Table 20). However, some names have since been validated and we currently accept 43 species names in Neofusicoccum. References: Phillips et al. (2013) (morphology, phylogeny, hosts), Dissanayake et al. (2016) (phylogeny, hosts, species numbers). Phyllosticta Pers., Traité champ. (Paris): 55, 147 (1818) Background Phyllosticta is an important coelomycetous genus of plant pathogens known to cause diseases in a wide range of host plants worldwide. Examples include citrus black spot, black rot of grapevines and banana freckle, which cause severe economic damage to their hosts (Baayen et al. 2002; Pu et al. 2008; Glienke et al. 2011; Wikee et al. 2013a, b, c). Some species have been reported as endophytes, saprobes or bio control agents. Species identification in Phyllosticta has historically been based on morphology, culture characters and host association. In recent decades molecular data have improved the knowledge of species relationships and taxonomic classifications and are expected to reveal novel cryptic species in some of the complex groups of Phyllosticta (Wikee et al. 2013a, b, c). 123 Author's personal copy 110 123 Fungal Diversity (2019) 94:41–129 Author's personal copy Fungal Diversity (2019) 94:41–129 b Fig. 19 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, GAPDH and TEF1-a sequence data of Curvularia species. Related sequences were obtained from GenBank. Eighty-nine strains are included in the analyses, which comprise 1996 characters including gaps. Tree was rooted with Bipolaris maydis (CBS 137271), B. microlaenae (CBS 280.91) and B. oryzae (MFLUCC 10-0715). The best scoring RAxML tree with a final likelihood value of - 13720.654431 is presented. The matrix had 716 distinct alignment patterns, with 19.91% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.23274, C = 0.300605, G = 0.240654, T = 0.226; substitution rates AC = 0.761255, AG = 2.478832, AT = 0.794435, CG = 0.897227, CT = 5.171218, GT = 1.000000; gamma distribution shape parameter a = 0.790494. RAxML bootstrap support values C 60% (BT) are shown respectively near the nodes. The scale bar indicates 0.02 changes per site. T, ET, IsoT IsoLT IsoPT LT , , , and NT indicate ex-type, ex-epitype, ex-isotype, exisolectotype, ex-isoparatype, ex-lectotype and ex-neotype strains, respectively Phyllosticta was introduced by Persoon (1818) and typified by P. convallariae Pers. Since then numerous species have been added to the genus and 3215 names are listed under Phyllosticta in Index Fungorum (30 Jan 2018). Sexual morphs are in Guignardia with 344 species names listed in Index Fungorum (30 Jan 2018). Following the introduction of the one-fungus one-name rule, Phyllosticta 111 (1818) was adopted as the correct name for this genus because it is older than Guignardia (1892) and names in Guignardia should be made synonyms of Phyllosticta (Sultan et al. 2011; Wikee et al. 2011, 2013a, b, c). Classification—Dothideomycetes, incertae sedis, Botryosphaeriales, Phyllostictaceae Type species—Phyllosticta convallariae Pers, Traité champ. (Paris): 148 (1818) Distribution—Worldwide Disease Symptoms—Normally Phyllosticta species cause small necrotic leaf lesions that are circular, brown to dark brown or sometimes reddish at the margin. Pycnidia can be found on the lesions and are usually black, globose to subglobose and semi immersed. After infection the leaf may become dry in the centre of the lesion and the infected tissue falls out leaving a hole (Glienke et al. 2011). When freckle disease occurs on banana species, pycnidia and ascomata formed on fruits give the lesion a sand paper texture. Leaves of banana turn yellow when infected with this Phyllosticta (Wikee et al. 2013a). Hosts—Phyllosticta species are mostly plant pathogens causing diseases in fruits and leaf spots on a broad range of Fig. 19 continued 123 Author's personal copy 112 Fungal Diversity (2019) 94:41–129 Fig. 20 First of 1000 most parsimonious trees resulting from analysis of combined ITS, TEF1-a, tub2 and RPB2 sequence data. Forty three strains were included in the analyses, which comprise 1829 characters including gaps. The tree was rooted with Botryosphaeria dothidea. (CBS 100564). Topology of the MP tree was similar to that of the ML and BI trees. The maximum parsimony dataset consisted of 1829 characters of which 1335 were constant, 241 variable characters were pasimony uninformative. Analysis of the remaining 253 parsimonyinformative characters resulted in 1000 equally most parsimonious trees with a length of 873 steps and CI = 0.674, RI = 0.762, HI = 0.326. The best scoring RAxML tree had a final likelihood value of - 7311.594985. The matrix had 583 distinct alignment patterns, with 14.54% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.214778, C = 0.295225, G = 0.272849, T = 0.217148; substitution rates AC = 1.184543, AG = 5.593626, AT = 1.053227, CG = 1.490317, CT = 11.314839, GT = 1.000000; gamma distribution shape parameter a = 0.472397. Bootstrap values for MP followed by ML are given at the nodes Thickened lines represent Bayesian posterior probability scores [ 0.95. Ex-type and ex-epitype isolates are in bold host plants including economically important crops and ornamentals such as citrus, banana, apple, grapes, cranberry, orchids, Ficus sp., Buxus sp. and maple amongst many others (Baayen et al. 2002; Glienke et al. 2011; Wikee et al. 2013a). parasite. The first monograph on Phyllosticta sensu stricto was by van der Aa (1973) using material collected in Europe and North America. He described and illustrated 46 species, and listed the sexual morphs for twelve species and the spermatial morphs for 17 species. In 2002 van der Aa & Vanev further revised the species in Phyllosticta, and accepted 190 epithets (Wikee et al. 2013a, b, c). Schoch et al. (2006) placed Phyllosticta in Botryosphaeriaceae in order Botryosphaeriales and this was accepted by Crous et al. (2006) and Liu et al. (2012). The family Phyllostictaceae (as Phyllostictei) was first Morphological based identification and diversity This genus has undergone many significant changes since its introduction. Phyllosticta species were considered to be Phoma-like foliar pathogens. On other plant parts Phyllosticta was regarded as a parasite and Phoma as a saprobe or wound 123 Author's personal copy Fungal Diversity (2019) 94:41–129 Table 20 Neofusicoccum. Details of the isolates used in the phylogenetic analyses 113 Species Isolate ITS TEF1-a tub-2 RPB2 N. algeriense CBS 137504* KJ657702 KJ657715 KX505915 N/A N. andinum CBS 117453* AY693976 AY693977 KX464923 KX464002 N. arbuti CBS 116131* AY819720 KF531792 KF531793 KX464003 N. austral CMW 6837* AY339262 AY339270 AY339254 EU339573 N. batangarum CBS 124924* FJ900607 FJ900653 FJ900634 FJ900615 N. braziliense CMM 1285 JX513628 JX513608 KC794030 N/A N. buxi CBS 116.75* KX464165 KX464678 N/A KX464010 N. cordaticola CBS 123634* EU821898 EU821868 EU821838 EU821928 N. corticosae CBS 120081* DQ923533 KX464682 KX464958 KX464013 N. cryptoaustrale CMW 23785* FJ752742 FJ752713 FJ752756 KX464014 N. eucalypticola CBS 115679* AY615141 AY615133 AY615125 N/A N. eucalyptorum CBS 115791* AF283686 AY236891 AY236920 N/A N. grevilleae CBS 129518* JF951137 N/A N/A N/A N. hellenicum CERC 1947* KP217053 KP217061 KP217069 N/A N. hongkongensis N. ilicii CERC 2973* CGMCC 3.18311* KX278052 KY350150 KX278157 KY817756 KX278261 KY350156 KX278283 N/A N. italicum MFLUCC 15-0900* KY856755 KY856754 N/A N/A N. kwambonambiense CBS 123639* EU821900 EU821870 EU821840 EU821930 N. lumnitzerae CMW 41469* KP860881 KP860724 KP860801 KU587925 N. luteum CBS 562.92 KX464170 KX464690 KX464968 KX464020 N. macroclavatum CBS 118223* DQ093196 DQ093217 DQ093206 KX464022 N. mangiferae CBS 118531* AY615185 DQ093221 AY615173 KX464023 N. mangroviorum CMW 41365* KP860859 KP860702 KP860779 KU587905 N. mediterraneum CBS 121718* GU251176 GU251308 N/A KX464024 N. microconidium CERC 3497* KX278053 KX278158 KX278262 MF410203 N. nonquaesitum CBS 126655* GU251163 GU251295 GU251823 KX464025 N. occulatum CBS 128008* EU301030 EU339509 EU339472 EU339558 N. parvum CBS 138823* AY236943 AY236888 AY236917 EU821963 N. pennatisporum MUCC 510* EF591925 EF591976 EF591959 N/A N. pistaciae CBS 595.76* KX464163 KX464676 KX464953 KX464008 N. pistaciarum CBS 113083* N. pistaciicola CBS 113089* KX464186 KX464199 KX464712 KX464727 KX464998 KX465014 KX464027 KX464033 N. protearum CBS 114176* AF452539 KX464720 KX465006 KX464029 N. pruni CBS 121112* EF445349 EF445391 KX465016 KX464034 N. ribis CBS 115475* AY236935 AY236877 AY236906 EU339554 N. sinense CGMCC 3.18315* KY350148 KY817755 KY350154 N/A N. sinoeucalypti CERC 2005* KX278061 KX278166 KX278270 KX278290 N. stellenboschiana CBS 110864* AY343407 AY343348 KX465047 KX464042 N. terminaliae CBS 125264 GQ471802 GQ471780 KX465053 KX464046 N. umdonicola CBS 123645* EU821904 EU821874 EU821844 EU821934 N. ursorum CMW 24480* FJ752746 FJ752709 KX465056 KX464047 N. viticlavatum CBS 112878* AY343381 AY343342 KX465058 KX464048 N. vitifusiforme CBS 110887* AY343383 AY343343 KX465061 KX464049 Botryosphaeria dothidea CBS 100564 KX464085 KX464555 KX464781 KX463951 Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold proposed by Fries (1849). This family name was re-instated by Wikee et al. (2013a, b, c) who revealed that it is sister to Botryosphaeriaceae. Species in Phyllosticta are recognised by the production of pycnida containing aseptate, hyaline, ovoid to ellipsoid or cylindrical conidia with a single apical appendage and 123 Author's personal copy 114 Fungal Diversity (2019) 94:41–129 Fig. 21 Phylogenetic tree generated by maximum likelihood analysis of combined ITS, TEF1, ACT, LSU and GPDH sequence data of Phyllosticta species. Sequences were obtained from GenBank. Fifty four strains are included in the analyses, which comprise 2739 characters including gaps. Single gene analyses were carried out to compare the topology of the tree and clade stability. Tree was rooted with Diplodia seriata (CMW8232) Tree topology of the Bayesian analysis was similar to the RAxML. The best scoring RAxML tree with a final likelihood value of = - 18593.839155 is presented. The matrix had 1110 distinct alignment patterns, with 37.85% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.209468, C = 0.292249, G = 0.275727, T = 0.222557; substitution rates AC = 1.099701, AG = 2.944335, AT = 1.274132, CG = 1.149823, CT = 6.450643, GT = 1.000000; gamma distribution shape parameter a = 0.456374. RAxML and Bayesian posterior probabilities values C 70% (BT) and 0.9 (PP) are shown respectively near the nodes covered by a mucus layer (van der Aa 1973; Wikee et al. 2013a). However, some Phyllosticta species, such as P. colocasiicola, P. minima, and P. sphaeropsoidea do not have an appendage or mucus layer. Furthermore these mucoid appendages may vary in size and shape according to the media on which the culture is grown, and sometimes with time it may disappear. Pycnidia are usually globose to subglobose, unilocular and closely connected on a 123 Author's personal copy Fungal Diversity (2019) 94:41–129 115 Table 21 Phyllosticta. Details of the isolates used in the phylogenetic analyses Species Isolate ITS LSU TEF-I ACT GAPDH P. abieticola CBS112067* KF170306 EU754193 – KF289238 – P. alliacea MUCC0014* AB454263 – – – – P. ampelicida ATCC200578* KC193586 – – KC193581 KC193584 P. ardisiicola NBRC102261* AB454274 – – – – P. aspidistricola NBRC102244* AB454260 – – – – P. beaumarisii CBS 535.87* AY042927 KF306229 KF289170 KF306232 KF289074 P. bifrenariae CBS 128855* JF343565 KF206209 JF343586 JF343649 JF433744 P. capitalensis IMI 260.576* JF261459 KF206222 JF261501 JF343641 JF343748 P. capitalensis CPC 18848* JF261465 KF206255 JF261507 KF289289 JF343776 P. cavendishii BRIP554196* JQ743562 – KF009743 KF014080 – P. citriasiana P. citribraziliensis CBS 120486* CBS 100098* FJ538360 FJ538352 KF206314 KF206221 FJ538418 FJ538410 FJ538476 FJ538468 JF343686 JF343691 P. citricarpa CBS 127454* JF343583 KF206306 JF343604 JF343667 JF343771 P. citrichinaensis ZJUCC 200956* JN791620 – JN791459 JN791533 – P. citrimaxima CPC 20276* KF170304 KF206229 KF289222 KF289300 KF289157 P. concentric CBS 937.70* FJ538350 KF206291 FJ538408 KF289257 JF411745 P. cordylinophila CPC 20261* KF170287 KF206242 KF289172 KF289295 KF289076 P. cussonia CPC 14875* JF343579 KF206278 JF343600 JF343663 JF343765 P. dendrobii CGMCC 3.18666* MF180193 MF180210 MF180202 MF180220 MF180229 P. elongate CBS 126.22* FJ538353 – FJ538411 FJ538469 KF289164 P. ericarum CBS 132534* KF206170 KF206253 KF289227 KF289291 KF289162 P. fallopiae MUCC0113* AB454307 – – – – P. foliorum CBS 447.68* KF170309 KF206287 KF289201 KF289247 KF289132 P. gaultheriae CBS 447.70* JN692543 KF206298 JN692531 KF289248 JN692508 P. gaultheriae CBS 447.70* JN692543 KF206298 JN692531 KF289248 JN692508 P. hostae CGMCC 3.14355* JN692535 – JN692524 JN692512 JN692504 P. hubeiensis P. hymenocallidicola CGMCC 3.14986* CBS 131309* JX025037 JQ044423 – JQ044443 JX025042 KF289211 JX025032 KF289242 JX025027 KF289142 P. hypoglossi CBS 434.92* FJ538367 KF206299 FJ538425 FJ538483 JF343695 P. ilicis-aquifolii CGMCC 3.14358* JN692538 – JN692526 JN692514 – P. illicii CGMCC 3.18670* MF180195 MF180212 MF180203 MF180221 – P. kerriae MAFF240047* AB454266 – – – – P. leucothoicola CBS 136073* AB454370 AB454370 – KF289310 – P. ligustricola MUCC0024* AB454269 – – AB704212 – P. maculate CPC18347* JP743570 – KF009700 KF014016 – P. mangifera-indica CPC 20274* KF170305 KF206240 KF289190 KF289296 KF289121 P. minima CBS 585.84* KF206176 KF206286 KF289204 KF289249 KF289135 P. musicola CBS123405* FJ538334 – FJ538392 FJ538450 – P. neopyrolae CPC 21879* AB454318 AB454241 – AB704233 – P. owaniana CBS 776.97* KJ538368 KF206293 FJ538426 KF289254 JF343767 P. pachysandricola MUCC 124* AB454317 AB454317 – AB704232 – P. parthenocissi P. paxistimae CBS111645* CBS 112527* EU683672 KF206172 – KF206320 JN692530 KF289209 JN692518 KF289239 – KF289140 P. podocarpicola CBS 728.79* KF206173 KF206295 KF289203 KF289252 KF289134 P. rhaphiolepidis MUCC 432* DQ632660 – – AB704242 – P. rubra CBS 111635* KF206171 EU754194 KF289198 KF289233 KF289129 P. schimae CGMCC 3.14354* JN692534 – JN692522 JN692510 JN692506 P. schimicola CGMCC 3.17319* KJ847426 – KJ847448 KJ847434 KJ854895 123 Author's personal copy 116 Fungal Diversity (2019) 94:41–129 Table 21 (continued) Species Isolate ITS LSU TEF-I ACT GAPDH P. styracicola CGMCC 3.14985* JX052040 – JX025045 JX025036 KF289141 P. telopeae CBS 777.97* KF206205 KF766384 KF289210 KF289255 KF289141 P. vaccinii ATCC 46255* NR147339 – KC193582 KC193580 KC193583 P. vacciniicola CPC18590* – KF206257 KF289229 KF289287 KF289165 P. vitis-rotundifoliae CGMCC 3.17322* KJ847428 – KJ847450 KJ847436 KJ847442 Diplodia seriata CMW8232 AY972105 – DQ280419 AY972111 – Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold subepidermal pseudostroma. Ascomata are globose to pyriform, unilocular with a central ostiole and erumpent through the host epidermis. There is a thin peridium with wall comprising few layers of angular cells. Asci are 8 spored, bitunicate, clavate to broadly ellipsoid with wide, obtusely rounded apex and tapering gradually to a small pedicel and with a well-developed ocular chamber. Ascospores are hyaline, aseptate, ellipsoid to limoniform, usually with mucilaginous caps and often surrounded by a mucilaginous sheath, sometimes slightly elongated and often multiguttulate or with a large single central guttule (van der Aa 1973; Wikee et al. 2013a). However, species cannot be identified reliably on the basis of morphological characters alone due to plasticity and overlapping of dimensions. Molecular based identification and diversity Molecular methods have been used in taxonomic studies of Phyllosticta to reveal phylogenetic relationships between the species and also to resolve species complexes within the genus (Wulandari et al. 2009; Glienke et al. 2011; Wikee et al. 2011). Combined DNA phylogenetic analysis based on ITS, intron-dominated loci of genes like TEF1-a, ACT and more conserved gene regions such as LSU and GAPDH are used to reconstruct the phylogenetic relationships between the species. We reconstruct the phylogeny of the genus Phyllosticta (Fig. 21) based on analyses of a combined ITS, TEF1-a, ACT, LSU and GAPDH sequence data. It contains recently introduced species and corresponds to previous studies. Recommended genetic marker (Genus level)—ITS Recommended genetic markers (Species level)—ITS, LSU, TEF, GAPDH and ACT Accepted number of species: There are 3208 species epithets in Index Fungorum (2019) under this genus, but 190 are currently accepted. References: Wulandari et al. (2009) (pathogens), Glienke et al. (2011) (taxonomy), Wikee et al. (2011, 2013a, b) 123 (review), Su and Cai (2012) (Phylogeny), Hyde et al. (2013) (taxonomy, phylogeny), Kirk et al. (2013) (genus accepted), Slippers et al. (2013) (phylogeny), Wijayawardene et al. (2014) (Outline, phylogeny), Wu et al. (2014) (species in banana) (Table 21). Discussion Since the introduction of molecular techniques, many plant pathogenic fungi have been shown to represent species complexes or shown to be of poly- or paraphyletic nature (Hyde et al. 2014, 2018a, b). Thus, resolving these concepts is of utmost importance for global plant trade (Hyde et al. 2011). The present project, which is the second paper of a series focused on fungi that are phytopathogens, aims to provide a backbone tree for genera as well as to provide updates of all currently accepted taxa. Several groups covered in this study are pathogens on plants that are neither used in agriculture nor forestry. As the knowledge of phytopathogenic fungi increases at a high pace, the readers can use this study as a starting point. Researchers who can cover any group that is not covered here or can provide insights are warmly invited to take part in future One Stop shop series by contacting the first author. Acknowledgements This work was funded by the grants of the National Natural Science Foundation of China (NSFC Grant Nos. 31670027, 31460011 and 30870009). Ruvishika S. Jayawardena would like to thank the National Research Council of Thailand grants Thailands’ Fungal Diversity, Solving Problems and Creating Biotechnological Products (Grant No. 61201321016) and Taxonomy, Diversity, Phylogeny and Evolution of fungi in Capnodiales (Grant No. 61215320024). 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 Dracena species’’ (Grant No. DBG6080013) 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 University of Mauritius for research support. Alan J.L. Phillips acknowledges the support from Biosystems and Integrative Sciences Institute (BioISI, FCT/UID/Multi/04046/ Author's personal copy Fungal Diversity (2019) 94:41–129 2013). José RC Oliveira-Filho, Gladstone A. da Silva and Tatiana B. Gibertoni would like to thank Associação Nordesta for field support, Capes-SIU (008/13) and Fundação de Amparo à Ciência e Technologia de Pernambuco (FACEPE, APQ-0375-2.03/15) for financial support and the Conselho Nacional de Desenvolvimento Cientı́fico e Technológico (CNPq) (307601/2015-3 and 312186/2016-9) for scholarships. Alistair R. McTaggart acknowledges the University of Queensland Development Fellowships (UQFEL1718905) and support from the Department of the Environment and Energy under the Australian Biological Resources Study (Grant No. RG18-43). Kuntida Phutthacharoen would like to thank the Royal Golden Jubilee PhD program under Thailand Research Fund for a personal grant (RGJ scholarship no. PHD/0002/2560). Wei Dong would like to acknowledge the National Natural Science Foundation of China (Project ID: NSF31500017 to Huang Zhang). Ruvishika S. Jayawardena would like to thank Dr. S. Pennycook, Dr. P. Kirk and Dr. O. 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Stud Mycol 76:1–29 Wingfield MJ, De Beer W, Slippers B, Wingfield BD, Groenewald JZ, Lombard L, Crous PW (2012) One fungus, one name promotes progressive plant pathology. Mol Plant Pathol 13:604–613 Woudenberg JHC, Groenewald JZ, Binder M, Crous PW (2013) Alternaria redefined. Stud Mycol 75:171–212 Woudenberg JHC, van der Merwe NA, Jurjević Ž, Groenewald JZ, Crous PW (2015) Diversity and movement of indoor Alternaria alternate across the mainland USA. Fungal Gen Biol 81:62–72 Wright JE, Blumenfeld SN (1984) New South Americal species of Phellinus (Hymenochaetaceae). Mycotaxon 21:413–425 Wu HX, Schoch CL, Boonmee S, Bahkali AH, Chomnunti P, Hyde KD (2011) A reappraisal of Microthyriaceae. Fungal Divers 51:189–248 Wu SP, Liu YX, Yuan J, Wang Y, Hyde KD, Liu ZY (2014) Phyllosticta species from banana (Musa sp.) in Chongqing and Guizhou provinces, China. Phytotaxa 188:135–144 Wulandari NF, To-anun C, Hyde KD, Durong LM, De Gruyter J, Meffert JP, Groenewald JZ, Crous PW (2009) Phyllosticta citriasianum sp nov., the causes of Citrus tan spot of Citrus maxima (Pamelo). Fungal Divers 34:23–39 Fungal Diversity (2019) 94:41–129 Ryvarden L (2004) Neotropical polypores: Part 1: introduction, Ganodermataceae & Hymenochaetaceae. Fungiflora Yang SL, Chung KR (2010) Transcriptional regulation of Elsinochrome phytotoxin biosynthesis by an EfSTE12 activator in the citrus scab pathogen Elsinoe fawecettii. Fungal Biol 114:64–73 Yang T, Groenewald JZ, Cheewangkoon R, Jami F, Abdollahzadeh J, Lombard L, Crous PW (2017) Families, genera, and species of Botryosphaeriales. Fungal Biol 121:322–346 Zan LF, Bao HY, Bau T, Li YA (2015) New antioxidant pyrano[4,3c][2]benzopyran-1,6-dione derivative from the medicinal mushroom Fomitiporia ellipsoidea. Nat Product Commun 10(2):315–316 Zhang N, Zhao S, Shen Q (2011a) A six-gene phylogeny reveals the evolution of mode of infection in the rice blast fungus and allied species. Mycologia 103:1267–1276 Zhang Y, Crous P, Schoch C, Bahkali A, Guo L, Hyde KD (2011b) A molecular, morphological and ecological re-appraisal of Venturiales—a new order of Dothideomycetes. Fungal Divers 51:249–277 Zhang W, Nan ZB, Liu GD (2013) First report of Limonomyces roseipellis causing pink patch on Bermudagrass in south China. Plant Dis 97:561 Zhang J, Dou Z, Zhou Y, He W, Zhang X, Zhang Y (2016) Venturia sinensis sp. nov. a new ventuarialean ascomycete from Khingan Mountains. Saudi J Biol Sci 23:592–597 Zhao Q, Xie XW, Shi YX, Chai AL, Li BJ (2016) Boeremia leaf and fruit spot of okra caused by Boeremia exigua in China. Can J Plant Pathol 38:395–399 Zhou LW (2014) Fulvifomes hainanensis sp. nov. and F. indicus comb.nov. (Hymenochaetales, Basidiomycota) evidenced by a combination of morphology and phylogeny. Mycoscience 55:70–77 Zhou LW (2015) Fulviformes imbricatus and F. thailandicus (Hymenochaetales, Basidiomycota): two new species from Thailand based on morphological and molecular evidence. Mycol Prog 14:article89 Zhou LW, Xue HJ (2012) Fomitiporia pentaphylacis and F. tenuitubus spp. nov. (Hymenochaetales, Basidiomycota) from Guangxi, southern China. Mycol Prog 11:907–913 Zhu L, Wang X, Huang F, Zhang J, Li H, Hyde KD, Ding D (2012) A destructive new disease of Citrus in China caused by Cryptosporiopsis citricarpa sp. nov. Plant Dis 96:804–812 Affiliations Ruvishika S. Jayawardena1,2 • Kevin D. Hyde1,2,3 • Rajesh Jeewon4 • Masoomeh Ghobad-Nejhad5 • Dhanushka N. Wanasinghe3,6 • NingGuo Liu2,16 • Alan J. L. Phillips7 • José Ribamar C. Oliveira-Filho8 • Gladstone A. da Silva8 • Tatiana B. Gibertoni8 • P. Abeywikrama2,9 • L. M. Carris10 • K. W. T. Chethana2,9 • A. J. Dissanayake2 • S. Hongsanan11 • S. C. Jayasiri2 • A. R. McTaggart12 • R. H. Perera2 • K. Phutthacharoen2 K. G. Savchenko13 • R. G. Shivas14 • Naritsada Thongklang2 • Wei Dong2,15 • DePing Wei2,15 • Nalin N. Wijayawardena2 • Ji-Chuan Kang1 123 • Author's personal copy Fungal Diversity (2019) 94:41–129 1 The Engineering Research Center of Southwest Biopharmaceutical Resources, Ministry of Education, Guizhou University, Guiyang 550025, People’s Republic of China 2 Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand 3 4 5 6 7 8 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 Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P.O. Box 15815-3538, Tehran 15819, Iran World Agroforestry Centre, East and Central Asia, Kunming 650201, Yunnan, People’s Republic of China Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Campo Grande, 1749-016 Lisbon, Portugal Departamento de Micologia, Universidade Federal de Pernambuco, Avenida da Engenharia, S/N - Cidade Universitária, Recife, PE 50740-600, Brazil 129 9 Beijing Key Laboratory of Environmet Friendly Management on Fruit Disease and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, People’s Republic of China 10 Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA 11 College of Life Science and Oceanography, ShenZhen University, 1068, Nanhai Avenue, Nanshan, Shenzhen 518055, China 12 Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4001, Australia 13 Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA 14 Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia 15 Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand 16 Faculty of Agriculture, National Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand 123

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One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26-50 (2019

One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26-50 (2019

One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26-50 (2019

One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26-50 (2019

One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26-50 (2019

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