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Showing papers by "Ali H. Bahkali published in 2015"


Journal ArticleDOI
TL;DR: The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups.
Abstract: Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.

458 citations


Journal ArticleDOI
Jian-Kui Liu1, Kevin D. Hyde1, Kevin D. Hyde2, E. B. Gareth Jones3, Hiran A. Ariyawansa1, Hiran A. Ariyawansa2, Darbhe J. Bhat4, Saranyaphat Boonmee1, Sajeewa S. N. Maharachchikumbura1, Sajeewa S. N. Maharachchikumbura2, Eric H. C. McKenzie5, Rungtiwa Phookamsak1, Rungtiwa Phookamsak2, Chayanard Phukhamsakda2, Chayanard Phukhamsakda1, Belle Damodara Shenoy6, Mohamed A. Abdel-Wahab7, Mohamed A. Abdel-Wahab3, Bart Buyck, Jie Chen1, K. W. Thilini Chethana1, Chonticha Singtripop2, Chonticha Singtripop1, Dong-Qin Dai2, Dong-Qin Dai1, Yu Cheng Dai8, Dinushani A. Daranagama2, Dinushani A. Daranagama1, Asha J. Dissanayake1, Mingkwan Doilom2, Mingkwan Doilom1, Melvina J. D’souza1, Melvina J. D’souza2, Xinlei Fan8, Ishani D. Goonasekara1, Kazuyuki Hirayama, Sinang Hongsanan1, Sinang Hongsanan2, Subashini C. Jayasiri1, Ruvishika S. Jayawardena2, Ruvishika S. Jayawardena1, Samantha C. Karunarathna1, Samantha C. Karunarathna2, Wen-Jing Li2, Wen-Jing Li1, Ausana Mapook1, Ausana Mapook2, Chada Norphanphoun1, Ka-Lai Pang9, Rekhani H. Perera1, Rekhani H. Perera2, Derek Peršoh10, Umpava Pinruan11, Indunil C. Senanayake2, Indunil C. Senanayake1, Sayanh Somrithipol11, Satinee Suetrong11, Kazuaki Tanaka12, Kasun M. Thambugala1, Kasun M. Thambugala2, Qing Tian2, Qing Tian1, Saowaluck Tibpromma1, Danushka Udayanga1, Danushka Udayanga2, Nalin N. Wijayawardene2, Nalin N. Wijayawardene1, Nalin N. Wijayawardene13, Dhanuska Wanasinghe1, Dhanuska Wanasinghe2, Komsit Wisitrassameewong1, Xiang Yu Zeng1, Faten A. Abdel-Aziz7, Slavomír Adamčík14, Ali H. Bahkali3, Nattawut Boonyuen11, Timur S. Bulgakov15, Philippe Callac16, Putarak Chomnunti2, Putarak Chomnunti1, Katrin Greiner17, Akira Hashimoto18, Akira Hashimoto12, Valérie Hofstetter, Ji Chuan Kang13, David P. Lewis12, Xinghong Li, Xingzhong Liu, Zuo Yi Liu, Misato Matsumura12, Peter E. Mortimer2, Gerhard Rambold17, Emile Randrianjohany, Genki Sato12, Veera Sri-indrasutdhi11, Cheng Ming Tian8, Annemieke Verbeken19, Wolfgang von Brackel, Yong Wang13, Ting-Chi Wen13, Jianchu Xu2, Ji Ye Yan, Rui-Lin Zhao, Erio Camporesi 
TL;DR: This paper is a compilation of notes on 110 fungal taxa, including one new family, 10 new genera, and 76 new species, representing a wide taxonomic and geographic range.
Abstract: This paper is a compilation of notes on 110 fungal taxa, including one new family, 10 new genera, and 76 new species, representing a wide taxonomic and geographic range. The new family, Paradictyoarthriniaceae is introduced based on its distinct lineage in Dothideomycetes and its unique morphology. The family is sister to Biatriosporaceae and Roussoellaceae. The new genera are Allophaeosphaeria (Phaeosphaeriaceae), Amphibambusa (Amphisphaeriaceae), Brunneomycosphaerella (Capnodiales genera incertae cedis), Chaetocapnodium (Capnodiaceae), Flammeascoma (Anteagloniaceae), Multiseptospora (Pleosporales genera incertae cedis), Neogaeumannomyces (Magnaporthaceae), Palmiascoma (Bambusicolaceae), Paralecia (Squamarinaceae) and Sarimanas (Melanommataceae). The newly described species are the Ascomycota Aliquandostipite manochii, Allophaeosphaeria dactylidis, A. muriformia, Alternaria cesenica, Amphibambusa bambusicola, Amphisphaeria sorbi, Annulohypoxylon thailandicum, Atrotorquata spartii, Brunneomycosphaerella laburni, Byssosphaeria musae, Camarosporium aborescentis, C. aureum, C. frutexensis, Chaetocapnodium siamensis, Chaetothyrium agathis, Colletotrichum sedi, Conicomyces pseudotransvaalensis, Cytospora berberidis, C. sibiraeae, Diaporthe thunbergiicola, Diatrype palmicola, Dictyosporium aquaticum, D. meiosporum, D. thailandicum, Didymella cirsii, Dinemasporium nelloi, Flammeascoma bambusae, Kalmusia italica, K. spartii, Keissleriella sparticola, Lauriomyces synnematicus, Leptosphaeria ebuli, Lophiostoma pseudodictyosporium, L. ravennicum, Lophiotrema eburnoides, Montagnula graminicola, Multiseptospora thailandica, Myrothecium macrosporum, Natantispora unipolaris, Neogaeumannomyces bambusicola, Neosetophoma clematidis, N. italica, Oxydothis atypica, Palmiascoma gregariascomum, Paraconiothyrium nelloi, P. thysanolaenae, Paradictyoarthrinium tectonicola, Paralecia pratorum, Paraphaeosphaeria spartii, Pestalotiopsis digitalis, P. dracontomelon, P. italiana, Phaeoisaria pseudoclematidis, Phragmocapnias philippinensis, Pseudocamarosporium cotinae, Pseudocercospora tamarindi, Pseudotrichia rubriostiolata, P. thailandica, Psiloglonium multiseptatum, Saagaromyces mangrovei, Sarimanas pseudofluviatile, S. shirakamiense, Tothia spartii, Trichomerium siamensis, Wojnowicia dactylidicola, W. dactylidis and W. lonicerae. The Basidiomycota Agaricus flavicentrus, A. hanthanaensis, A. parvibicolor, A. sodalis, Cantharellus luteostipitatus, Lactarius atrobrunneus, L. politus, Phylloporia dependens and Russula cortinarioides are also introduced. Epitypifications or reference specimens are designated for Hapalocystis berkeleyi, Meliola tamarindi, Pallidocercospora acaciigena, Phaeosphaeria musae, Plenodomus agnitus, Psiloglonium colihuae, P. sasicola and Zasmidium musae while notes and/or new sequence data are provided for Annulohypoxylon leptascum, A. nitens, A. stygium, Biscogniauxia marginata, Fasciatispora nypae, Hypoxylon fendleri, H. monticulosum, Leptosphaeria doliolum, Microsphaeropsis olivacea, Neomicrothyrium, Paraleptosphaeria nitschkei, Phoma medicaginis and Saccotheciaceae. A full description of each species is provided with light micrographs (or drawings). Molecular data is provided for 90 taxa and used to generate phylogenetic trees to establish a natural classification for species.

304 citations


Journal ArticleDOI
TL;DR: An updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the class are provided and new links between sexual and asexual genera and thus synonymies are provided.
Abstract: Sordariomycetes is one of the largest classes of Ascomycota and is characterised by perithecial ascomata and inoperculate unitunicate asci. The class includes many important plant pathogens, as well as endophytes, saprobes, epiphytes, and fungicolous, lichenized or lichenicolous taxa. The class includes freshwater, marine and terrestrial taxa and has a worldwide distribution. This paper provides an updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the class. Based on phylogeny and morphology we introduced three subclasses; Diaporthomycetidae, Lulworthiomycetidae and Meliolomycetidae and five orders; Amplistromatales, Annulatascales, Falcocladiales, Jobellisiales and Togniniales. The outline is based on literature to the end of 2014 and the backbone tree published in this paper. Notes for 397 taxa with information, such as new family and genera novelties, novel molecular data published since the Outline of Ascomycota 2009, and new links between sexual and asexual genera and thus synonymies, are provided. The Sordariomycetes now comprises six subclasses, 28 orders, 90 families and 1344 genera. In addition a list of 829 genera with uncertain placement in Sordariomycetes is also provided.

266 citations


Journal ArticleDOI
TL;DR: The Halosphaeriaceae remains the largest family of marine fungi with 141 species in 59 genera, while the most specious genera are Aspergillus, Penicillium and the yeast genus Candida.
Abstract: This paper lists the accepted names and classification of marine fungi, updating the scheme presented in 2009. The classification includes 1,112 species (in 472 genera): Ascomycota 805 (in 352 genera), Basidiomycota 21 species (in 17 genera), Chytridiomycota and related phyla 26 species (in 13 genera), Zygomycota three (in two genera), Blastocladiomycota one species (one genus), asexual morphs of filamentous fungi 43 (in 26 genera); and marine yeasts: Ascomycota 138 species (in 35 genera), Basidiomycota 75 species (in 26 genera). These fungi belong to 129 families and 65 orders. The Halosphaeriaceae remains the largest family of marine fungi with 141 species in 59 genera, while the most specious genera are Aspergillus (47 species), Penicillium (39 species) and the yeast genus Candida (64 species). The review includes details of recent higher order nomenclature changes, and accounts of new families, genera and species described over the past 5 years.

231 citations


Journal ArticleDOI
TL;DR: The classification of subclass Xylariomycetidae is revisited with additional collections and phylogeny based on novel rDNA sequence data, and the orders Amphisphaeriales and Xylariales are accepted based on morphological and phylogenetic evidence.
Abstract: The classification of subclass Xylariomycetidae is revisited with additional collections and phylogeny based on novel rDNA sequence data. Phylogenetic inferences are provided and are based on analysis of 115 sequence data, including new data for 27 strains. An updated outline to the subclass is presented based on the phylogenies and comprises two orders, 18 families and 222 genera. An account of each order, family and genus in the subclass is given. We accept the orders Amphisphaeriales and Xylariales based on morphological and phylogenetic evidence. Amphisphaeriales comprises Amphisphaeriaceae, Bartaliniaceae fam. nov., Clypeosphaeriaceae, Discosiaceae fam. nov., Pestalotiopsidaceae fam. nov. and Phlogicylindriaceae fam. nov. Xylariales comprises Apiosporaceae, Cainiaceae, Coniocessiaceae, Diatrypaceae, Graphostromataceae (doubtful), Hyponectriaceae, Iodosphaeriaceae, Lopadostomaceae fam. nov., Melogrammataceae, Pseudomassariaceae fam. nov., Vialaeaceae and Xylariaceae. The new genera and species introduced are Arthrinium hyphopodii, A. subglobosa, Cainia anthoxanthis, Ciferriascosea gen. nov., C. fluctamurum, C. rectamurum, Discosia neofraxinea, D. pseudopleurochaeta, Hyalotiella rubi, Seimatosporium cornii, S. ficeae, S. vitis and Truncatella spartii.

170 citations


Journal ArticleDOI
TL;DR: Salinity caused great alterations in the endogenous levels of growth hormones with abscisic acid showing increment and antioxidant enzymes like superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase exhibited great variation with salinity treatment.

115 citations


Journal ArticleDOI
TL;DR: Phylogenetic analyses show that species of Astrosphaeriella can be distinguished in at least three families, and a new family,Astrosphaeriellaceae, is introduced to accommodate these taxa.
Abstract: Astrosphaeriella sensu lato is a common genus occurring on bamboo, palms and stout grasses. Species of Astrosphaeriella have been collected from various countries in tropical, subtropical or temperate regions. In Asia, species have been collected in Brunei, China, Indonesia, Japan, Philippines and Vietnam. There have been several morphological studies on Astrosphaeriella, but molecular work and phylogenetic analyses are generally lacking. Taxa included in Astrosphaeriella were characterized in three main groups 1) typical Astrosphaeriella species (sensu stricto) having carbonaceous, erumpent, conical ascostromata 2) atypical Astrosphaeriella species (sensu lato) having immersed, coriaceous ascostromata with short to long papilla and 3) lophiostoma-like species having immersed ascostromata with slit-like openings. Some of the latter Astrosphaeriella species, having slit-like openings, have been transferred to Fissuroma and Rimora in Aigialaceae. In this study five type specimens of Astrosphaeriella were loaned from herbaria worldwide and re-examined and are re-described and illustrated. Collections of Astrosphaeriella were also made in Thailand and morphologically examined. Pure cultures were obtained from single spores and used in molecular studies. The asexual morph was induced on sterile bamboo pieces placed on water agar. Phylogenetic analyses of combined LSU, SSU and TEF1 sequence data of astrosphaeriella-like species using Bayesian, Maximum parsimony (MP) and Randomized Accelerated Maximum Likelihood (RAxML) analyses were carried out. Phylogenetic analyses show that species of Astrosphaeriella can be distinguished in at least three families. Species of Astrosphaeriella sensu stricto with erumpent, carbonaceous ascostromata, form a strongly supported clade with Pteridiospora species and a new family, Astrosphaeriellaceae, is introduced to accommodate these taxa. The genera are revised and Astrosphaeriella bambusae, A. neofusispora, A. neostellata, A. thailandica, A. thysanolaenae and Pteridiospora chiangraiensis are introduced as new species. Astrosphaeriella exorrhiza is reported on a dead stem of Thysanolaena maxima and is the first record for Thailand. Reference specimens for A. fusispora and A. tornata are designated to stabilize the taxonomy of Astrosphaeriella. The coelomycetous asexual morph of A. bambusae is reported and forms hyaline, globose to subglobose, aseptate conidia. Species of Astrosphaeriella sensu lato with immersed, coriaceous ascostromata, with short to long papilla and striate ascospores, form a sister clade with Tetraplosphaeriaceae. The genus Pseudoastrosphaeriella is introduced to accommodate some of these taxa with three new species and three new combinations, viz. P. aequatoriensis, P. africana, P. bambusae, P. longicolla, P. papillata and P. thailandensis. A new family Pseudoastrosphaeriellaceae is introduced to accommodate this presently monotypic lineage comprising Pseudoastrosphaeriella. The asexual morph of P. thailandensis is described. Astrosphaeriella bakeriana forms a distinct clade basal to Aigialaceae. Astrosphaeriella bakeriana is excluded from Astrosphaeriella and a new genus Astrosphaeriellopsis, placed in Dothideomycetes genera incertae sedis, is introduced to accommodate this taxon. Fissuroma aggregata (Aigialaceae) is re-visited and is shown to be a cryptic species. Three new species of Fissuroma and a new combination are introduced based on morphology and phylogeny viz. F. bambusae, F. fissuristoma, F. neoaggregata and F. thailandicum.

62 citations


Journal ArticleDOI
TL;DR: Multi-gene analysis coupled with morphology showed that Colletotrichum aenigma, C. hebeiense sp.
Abstract: Grapevine anthracnose is an important disease, responsible for mild to severe yield losses in grape production, and is also an important post harvest disease. The disease was studied in vineyards in six provinces in China, with 34 isolates obtained from diseased grapes. Multi-gene (ACT, ITS, GAPDH, TUB2 and CHS) analysis coupled with morphology showed that Colletotrichum aenigma, C. hebeiense sp. nov. and C. viniferum were associated with grapevine anthracnose in China. Colletotrichum aenigma is reported for the first time as associated with grapevine anthracnose. Colletotrichum hebeiense is a new species introduced here. Pathogenicity testing showed that all species can infect grapes, causing anthracnose however, virulence of species and isolates showed great variation. Phylogenetic analysis showed that C. viniferum is a cryptic species and its taxonomy needs to be resolved in the future.

62 citations


Journal ArticleDOI
TL;DR: Multi-locus phylogenies together with morphology robustly support the monophyletic nature of Leptosphaeriaceae among the other families in Pleosporales, and the inclusion of the genera Alternariaster, Heterospora, LePTosphaeria, Paraleptoshaeria, Sphaerellopsis, Subplenodomus, Plenidomus and three novel genera are established.
Abstract: Leptosphaeriaceae is a family in the order Pleosporales comprising economically important plant pathogens. Species may also be endophytes or saprobes on various host plants. In recent classifications Alternariaster, Leptosphaeria, Neophaeosphaeria, Paraleptosphaeria, Heterospora, Subplenodomus and Plenodomus were included in the family. The taxonomy of genera and species in Leptosphaeriaceae has been problematic due to the lack of understanding of the importance of morphological characters used to distinguish taxa, as well as the lack of reference strains. In order to establish evolutionary relationships and to provide a backbone tree for Leptosphaeria and allied genera, we sequenced the 18S nrDNA, 28S nrDNA, ITS, RPB2, TEF and ACT gene regions of Leptosphaeriaceae species and analysed this data. Multi-locus phylogenies together with morphology robustly support the monophyletic nature of Leptosphaeriaceae among the other families in Pleosporales, and the inclusion of the genera Alternariaster, Heterospora, Leptosphaeria, Paraleptosphaeria, Sphaerellopsis, Subplenodomus, Plenodomus and three novel genera Alloleptosphaeria, Neoleptosphaeria and Pseudoleptosphaeria. Five new species, Alternariaster centaureae-diffusae, Leptosphaeria cichorium, Paraleptosphaeria rubi, Plenodomus guttulatus and P. salviae are introduced. An account of sexual morph of Alternariaster centaureae-diffusae is provided, and the sexual morph of Leptosphaeria doliolum is re-described and illustrated using modern concepts from fresh collections. A novel family Neophaeosphaeriaceae is established to accommodate the genus Neophaeosphaeria and its species.

51 citations


Journal ArticleDOI
TL;DR: In this article, the authors describe ten new taxa for science using mostly both morphological and molecular data, including Ceramothyrium ficus (Chaetothyriales, Eurotiomycetes), Lachnum fusiforme (Leotiomycets, Helotiales), four new species in Dothideomycete, namely Micropeltis dendrophthoes (Microthyriales), Montagnula bellevaliae and M. scabiosae (Pleosporales), Scorias mangiferae

43 citations


Journal ArticleDOI
TL;DR: The type species of 26 genera of the family Melanommataceae are re-described and illustrated, and a multi-gene phylogeny based on maximum likelihood and Bayesian analyses of LSU, SSU, RPB2 and EF-1α sequence data of species of Melanomataceae is provided.
Abstract: The family Melanommataceae is widespread in temperate and subtropical regions and species invariably occur on twigs or bark of various woody plants in terrestrial, marine or freshwater habitats. In this paper, the type species of 26 genera of the family are re-described and illustrated. A multi-gene phylogeny based on maximum likelihood and Bayesian analyses of LSU, SSU, RPB2 and EF-1 alpha sequence data of species of Melanommataceae is provided. The new genera, Muriformistrickeria, Pseudostrickeria and Thysanolaenae are introduced. Anomalemma is synonymized under Exosporiella. Acrocordiopsis, Astrosphaeriella, Beverwykella, Caryosporella, Sporidesmiella and Pseudotrichia are excluded from Melanommataceae based on molecular phylogenetic analyses. Presently, 20 genera are accepted in Melanommataceae. Based on the phylogenetic data, five new species, Byssosphaeria siamensis, Herpotrichia vaginatispora, Pseudostrickeria muriformis, Pseudostrickeria ononidis and Muriformistrickeria rubi, are introduced.

Journal ArticleDOI
22 Apr 2015-PLOS ONE
TL;DR: Molecular variations to adapt to different Cf genes in an isolated C. fulvum population in Japan are novel but overall follow similar patterns as those observed in populations from other parts of the world.
Abstract: Leaf mold of tomato is caused by the biotrophic fungus Cladosporium fulvum which complies with the gene-for-gene system. The disease was first reported in Japan in the 1920s and has since been frequently observed. Initially only race 0 isolates were reported, but since the consecutive introduction of resistance genes Cf-2, Cf-4, Cf-5 and Cf-9 new races have evolved. Here we first determined the virulence spectrum of 133 C. fulvum isolates collected from 22 prefectures in Japan, and subsequently sequenced the avirulence (Avr) genes Avr2, Avr4, Avr4E, Avr5 and Avr9 to determine the molecular basis of overcoming Cf genes. Twelve races of C. fulvum with a different virulence spectrum were identified, of which races 9, 2.9, 4.9, 4.5.9 and 4.9.11 occur only in Japan. The Avr genes in many of these races contain unique mutations not observed in races identified elsewhere in the world including (i) frameshift mutations and (ii) transposon insertions in Avr2, (iii) point mutations in Avr4 and Avr4E, and (iv) deletions of Avr4E, Avr5 and Avr9. New races have developed by selection pressure imposed by consecutive introductions of Cf-2, Cf-4, Cf-5 and Cf-9 genes in commercially grown tomato cultivars. Our study shows that molecular variations to adapt to different Cf genes in an isolated C. fulvum population in Japan are novel but overall follow similar patterns as those observed in populations from other parts of the world. Implications for breeding of more durable C. fulvum resistant varieties are discussed.

Journal ArticleDOI
TL;DR: A phylogenetic analysis based on combined LSU, SSU and ITS sequence data showed that M. galatellae forms a distinct lineage in Phaeosphaeriaceae.
Abstract: Muriphaeosphaeria galatellae was collected from Galatella villosa in Russia and is introduced as a novel monotypic genus and species in the family Phaeosphaeriaceae (Pleosporales). Muriphaeosphaeria is distinct from other genera of the family Phaeosphaeriaceae by its unique suite of characters such as, superficial ascomata with an ascomatal wall comprising thin-walled brown cells, cellular pseudoparaphyses, muriform ascospores; and conidiomata with a thick hyaline inner wall layer producing cylindrical to subclavate, 1-3-transversely septate, brown conidia. The asexual morph of M. galatellae developed in cultures when grown on sterilized pine needles and bamboo pieces. A phylogenetic analysis based on combined LSU, SSU and ITS sequence data showed that M. galatellae forms a distinct lineage in Phaeosphaeriaceae. The new genus and species are introduced and compared with other taxa in the family.

Journal ArticleDOI
TL;DR: This study observed three specimens of Seimatosporium from Russia and they are characterized by morphological and sequence data, and can be distinguished from similar and related species by phenotypic conidial characters and phylogenetic analyses.
Abstract: The genus Seimatosporium is saprobic or pathogenic on plants, and are 'pestalotioid fungi'. The genus presently belongs in Discosiaceae (Amphisphaeriales) and includes 78 species epithets. In this study, we observed three specimens of Seimatosporium from Russia and they are characterized by morphological and sequence data. We analyzed combined ITS and LSU gene sequence data of 42 species representing the genera Discostroma (7), Sarcostroma (2) and Seimatosporium (32, including the three new strains) with Pseudopestalotiopsis theae as the outgroup taxon. One isolate from dead branches of Physocarpus opulifolius is unique and is introduced as Seimatosporium physocarpi sp. nov., in this paper. It can be distinguished from similar and related species by phenotypic conidial characters and phylogenetic analyses. A specimen from Rosa kalmiussica Chrshan. & Lasebna (often included in Rosa canina sensu lato) is designated as an epitype for S. rosae, the type of the genus. In addition, a collection of S. lichenicola is described, illustrated and compared with other species in the genus.

Journal ArticleDOI
01 Sep 2015
TL;DR: In this article, the same species of Meliola and one new species of Irenopsis are also introduced with molecular data and provided the most populated phylogenetic tree of Meliolomycetidae to date.
Abstract: The order Meliolales comprises the families Armatellaceae and Meliolaceae. These are black mildews that grow on the surface of host plants, often regarded as minor plant pathogens. In this study, types or specimens of 17 genera of Armatellaceae and Meliolaceae were borrowed from herbaria and re-examined. Armatella is accepted in Armatellaceae and Amazonia, Appendiculella, Asteridiella, Cryptomeliola, Endomeliola, Irenopsis and Meliola are accepted in the family Meliolaceae. Laeviomeliola is synonymized under Meliola. Ceratospermopsis, Ectendomeliola, Haraea, Hypasteridium, Leptascospora, Metasteridium, Ophiociliomyces, Ophioirenina, Ophiomeliola, Parasteridium, Pauahia, Pleomeliola, Pleomerium, Prataprajella, Ticomyces, Urupe and Xenostigme are excluded from Meliolaceae, and are treated as doubtful genera or placed in ascomycetes genera incertae sedis. The type species of each genus is re-described and illustrated with photomicrographs. Notes are provided and comparisons made. Two new species of Meliola and one new species of Irenopsis are also introduced with molecular data and we provide the most populated phylogenetic tree of Meliolomycetidae to date. Meliola thailandicum was found on Dimocarpus longan (Sapindales) and Acacia auriculiformis (Fabales) and confirmed to be the same species in the molecular analyses. This has important implications as the several hundred Meliola species are recognized based on host associations. Thus the same species being recorded from two unrelated hosts sheds doubt on Meliola species being host-specific.

01 Jan 2015
TL;DR: A new order, Zeloasperisporiales is introduced to accommodate the family Zelo Jasperisporiaceae, an epiphytic genus that forms small black dots on the surface of living or dead fallen leaves, although it rarely causes any damage to the host.
Abstract: Neomicrothyrium is an epiphytic genus that forms small black dots on the surface of living or dead fallen leaves, although it rarely causes any damage to the host. Based on its flattened thyriothecia, it was considered that Neomicrothyrium belongs in the order Microthyriales, a group of fungi that is relatively poorly studied. “Microthyriaceae”-like taxa appearing as small black dots on leaves were collected in Chiang Rai Province, Thailand, and studied using morphological characterization and phylogenetic analyses. As a result of molecular and morphological study, we established that Neomicrothyrium is linked to the asexual genus Zeloasperisporium and that we had collected two new taxa. Two new species, Zeloasperisporium ficusicola and Z. wrightiae are therefore introduced in this study based on morphology and phylogeny. Neomicrothyrium is linked to Zeloasperisporium and is therefore synonymized under the older name Zeloasperisporium. Phylogenetic analyses of combined LSU and SSU rDNA sequence data indicate that Zeloasperisporiaceae belong in the class Dothideomycetes, but clusters with Natipusillales in a distinct lineage from Microthyriales. We therefore introduce a new order, Zeloasperisporiales to accommodate the family Zeloasperisporiaceae. The life cycle of Zeloasperisporium species is remarkable. The sexual morph produces ascomata on the leaf surface and appears to lack any other structures and it is unclear how the ascomata obtain nutrients. The asexual morph produces conidia which can be found on the surface of plants, or in air, but it is also unclear how conidia obtain their nutrients. In this study, isolates from the sexual morph produced asexual morphs in culture.

Journal ArticleDOI
TL;DR: A new ascomycete species, Bambusicola loculata, inhabiting decaying bamboo, is introduced based on morpho-molecular studies and compared with other morphologically and phylogenetically similar species.
Abstract: A new ascomycete species, Bambusicola loculata, inhabiting decaying bamboo, is introduced based on morpho-molecular studies. Bambusicola loculata is characterized by immersed, dark, stromatic and loculate ascostromata, bitunicate, cylindrical-clavate asci and 1-septate, hyaline, narrowly fusiform ascospores, surrounded by an inconspicuous mucilaginous sheath. Maximum likelihood and Bayesian analyses of combined LSU, SSU, RPB2 and TEF1 gene sequence data as well as morphological characters show that our new taxon belongs to Bambusicola, Bambusicolaceae. The new species is compared with other morphologically and phylogenetically similar species.

Journal ArticleDOI
TL;DR: A new genus and species is introduced to accommodate this new lineage of Aquapteridospora, a hyphomycete with polyblastic conidiogenous cells with several sympodial proliferations, bearing tiny, protuberant, circular scars and fusiform conidia.

01 Jan 2015
TL;DR: Ten new asexual taxa (Phaeosphaeriaceae) were collected from terrestrial habitats in Italy and introduced and combined ITS and LSU sequence data from the new taxa together with those from GenBank were analyzed to establish the phylogenetic placement of these taxa.
Abstract: Species of Phaeosphaeriaceae, especially the asexual taxa, are common plant pathogens that infect many important economic crops. Ten new asexual taxa (Phaeosphaeriaceae) were collected from terrestrial habitats in Italy and are introduced in this paper. In order to establish the phylogenetic placement of these taxa within Phaeosphaeriaceae we analyzed combined ITS and LSU sequence data from the new taxa, together with those from GenBank. Based on morphology and molecular data, Poaceicola gen. nov. is introduced to accommodate the new species Po. arundinis (type species), Po. bromi and Po. elongata. The new species Parastagonospora dactylidis, P. minima, P. italica, P. uniseptata and P. allouniseptata, Septoriella allojunci and Wojnowicia spartii are also introduced with illustrated accounts and compared with similar taxa. We also describe an asexual morph of a Nodulosphaeria species for the first time.

Journal ArticleDOI
TL;DR: Two new species referable to Vagicola, Phaeosphaeriaceae are introduced in this paper based on analyses of LSU and ITS sequence data and their unique morphology.
Abstract: Phaeosphaeriaceae is a large and important family in the order Pleosporales, comprising economically important plant pathogens. Species may also be endophytes or saprobes on plant hosts. Two new species referable to Vagicola, Phaeosphaeriaceae are introduced in this paper based on analyses of LSU and ITS sequence data and their unique morphology. Most Phaeosphaeriaceae species grow on monocotyledons; Vagicola dactylidis and V. chlamydospora are also saprobic on grasses (Poaceae). Vagicola chlamydospora formed asexual structures in a culture. The new species are described and illustrated and compared with other taxa.

Journal ArticleDOI
TL;DR: Zeloasperisporium is an epiphytic genus that forms small black dots on the surface of living or dead fallen leaves, although it rarely causes any damage to the host.



01 Jan 2015
TL;DR: In this paper, the authors reported the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum, Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici.
Abstract: Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non- or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum, Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici. In these fungi, we identified 1740 gene models containing 2795 DMs obtained by an alignment-based gene prediction method. The contribution of sequencing errors to DMs was minimized by analyses of resequenced genomes to obtain a refined dataset of 924 gene models containing 1666 true DMs. The frequency of pseudogenes varied from 1% to 5% in the gene catalogues of these fungi, being the highest in the asexually reproducing fungus C. fulvum (4.9%), followed by D. septosporum (2.4%) and V. dahliae (2.1%). The majority of pseudogenes do not represent recent gene duplications, but members of multi-gene families and unitary genes. In general, there was no bias for pseudogenization of specific genes in the six fungi. Single exceptions were those encoding secreted proteins, including proteases, which appeared more frequently pseudogenized in C. fulvum than in D. septosporum. Most pseudogenes present in these two phylogenetically closely related fungi are not shared, suggesting that they are related to adaptation to a different host (tomato versus pine) and lifestyle (biotroph versus hemibiotroph).

Journal ArticleDOI
Hiran A. Ariyawansa1, Kevin D. Hyde, Subashini C. Jayasiri1, Bart Buyck2, K. W. Thilini Chethana1, Dong-Qin Dai3, Dong-Qin Dai1, Yu Cheng Dai4, Dinushani A. Daranagama1, Dinushani A. Daranagama3, Ruvishika S. Jayawardena1, Robert Lücking5, Masoomeh Ghobad-Nejhad6, Tuula Niskanen7, Kasun M. Thambugala1, Kerstin Voigt8, Rui-Lin Zhao3, Guo-Jie Li3, Mingkwan Doilom1, Mingkwan Doilom3, Saranyaphat Boonmee1, Zhu L. Yang3, Qing Cai3, Yang-Yang Cui3, Ali H. Bahkali9, Jie Chen4, Jie Chen1, Bao-Kai Cui4, Jia-Jia Chen4, Monika C. Dayarathne1, Monika C. Dayarathne3, Asha J. Dissanayake1, Anusha H. Ekanayaka1, Akira Hashimoto10, Akira Hashimoto11, Sinang Hongsanan1, Sinang Hongsanan3, E. B. Gareth Jones9, Ellen Larsson12, Wen-Jing Li1, Qi-Rui Li1, Jian-Kui Liu1, Zong-Long Luo13, Sajeewa S. N. Maharachchikumbura1, Ausana Mapook3, Ausana Mapook1, Eric H. C. McKenzie14, Chada Norphanphoun1, Sirinapa Konta1, Ka-Lai Pang15, Rekhani H. Perera1, Rekhani H. Perera3, Rungtiwa Phookamsak1, Rungtiwa Phookamsak3, Chayanard Phukhamsakda1, Umpava Pinruan, Emile Randrianjohany, Chonticha Singtripop1, Chonticha Singtripop3, Kazuaki Tanaka10, Cheng Ming Tian4, Saowaluck Tibpromma3, Saowaluck Tibpromma1, Mohamed A. Abdel-Wahab16, Mohamed A. Abdel-Wahab9, Dhanushka N. Wanasinghe3, Dhanushka N. Wanasinghe1, Nalin N. Wijayawardene1, Nalin N. Wijayawardene17, Jin-Feng Zhang1, Huang Zhang18, Faten A. Abdel-Aziz16, Mats Wedin19, Martin Westberg19, Joseph F. Ammirati20, Timur S. Bulgakov21, Diogo Xavier Lima22, Tony M. Callaghan23, Philipp Callac24, Cheng-Hao Chang25, Luis Fernando Coca26, Manuela Dal-Forno27, Veronika Dollhofer, K. Fliegerová28, Katrin Greiner29, Gareth W. Griffith23, Hsiao-Man Ho25, Valérie Hofstetter, Rajesh Jeewon30, Ji Chuan Kang17, Ting-Chi Wen17, Paul M. Kirk7, Ilkka Kytövuori31, James D. Lawrey27, Jia Xing, Hong Li, Zou Yi Liu, Xingzhong Liu3, Kare Liimatainen31, H. Thorsten Lumbsch, Misato Matsumura10, Bibiana Moncada32, Salilaporn Nuankaew, Sittiporn Parnmen, André Luiz Cabral Monteiro de Azevedo Santiago22, Sujinda Sommai, Yu Song3, Carlos A. F. De Souza22, Cristina Maria de Souza-Motta22, Hong Yan Su13, Satinee Suetrong33, Yong Wang17, Syuan-Fong Wei25, Ting Chi Wen17, Hai Sheng Yuan3, Li-Wei Zhou3, Martina Réblová, Jacques Fournier, Erio Camporesi, J. Jennifer Luangsa-ard, Kanoksri Tasanathai, Artit Khonsanit, Donnaya Thanakitpipattana, Sayanh Somrithipol, Paul Diederich, Ana M. Millanes34, Ralph S. Common, Marc Stadler, Ji Ye Yan, Xinghong Li, Hye Won Lee35, Thi Thuong Thuong Nguyen35, Hyang Burm Lee35, Eliseo Battistin36, Orlando Marsico, Alfredo Vizzini37, Jordi Vila, Enrico Ercole37, Ursula Eberhardt38, Giampaolo Simonini, Hua-An Wen3, Xin-Hua Chen39, Otto Miettinen31, Viacheslav Spirin31, Hernawati40 
TL;DR: In this paper, taxonomic and phylogenetic contributions to fungal taxa are described and annotated for the first time in a taxonomic context.Erratum to: Fungal Diversity Notes 111−252
Abstract: Erratum to: Fungal Diversity Notes 111–252 - taxonomic and phylogenetic contributions to fungal taxa.

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TL;DR: Fumonisin was produced by all of the studied Fusarium isolates, except F. oxysporum, at a concentration of over 1 μg/mL, indicating non-agreement between morphological and molecular identification of the isolates.
Abstract: Infesting Fusarium species isolated from banana fruit samples were identified and quantified by morphological, mycotoxicological and molecular tools. A total of 19 Fusarium isolates were obtained: F. semitectum was most predominant (26%), followed by F. proliferatum (16%), F. circinatum (16%), F. chlamydosporum (10.5%), F. solani (10.5%), F. oxysporum (10.5%) and F. thapsinum (5%). Fumonisin B1, deoxynivalenol and zearalenone contents were assayed by high-performance liquid chromatography (HPLC). Seventeen isolates, belonging to F. chlamydosporum, F. circinatum, F. semitectum, F. solani, F. thapsinum, F. proliferatum and Fusarium spp., produced mycotoxins when cultured on rice medium. Fumonisin was produced by all of the studied Fusarium isolates, except F. oxysporum, at a concentration of over 1 μg/mL. F. citrinium isolates 4 and 5 and F. solani isolate 3 were the most potent producers of deoxynivalenol. We compared the 19 Fusarium isolates based on the bands amplified by 10 microsatellite primers. Of these, seven primers, (TCC)5, (TGG)5, (GTA)5, (ATG)5, (TAC)5, (TGC)5 and (TGT)5, yielded a high number of bands and different mean number of alleles. The similarity level between isolates was calculated using a simple matching coefficient. Dendrograms were constructed by the unweighted pair-group method with arithmetical averages (UPGMA). Two main clusters were observed. The interspecific genetic similarity between Fusarium spp. isolates was between 40% and 58% and the intraspecific similarity from 58% to 100%, indicating a high degree of genetic diversity in the tested isolates. Some unexpected genetic similarities were observed among the isolates, indicating non-agreement between morphological and molecular identification of the isolates.

Journal ArticleDOI
TL;DR: Morphology and combined phylogenetic analysis of ITS, LSU, β-tubulin and RPB2 sequence data, showed it to be a new Rhopalostroma species introduced herein as R. brevistipitatum.
Abstract: Rhopalostroma species were collected from Northern Thailand and subjected to morph-molecular analysis . One species possessed small, clavate stromata, with short and stout stipes, asci with an amyloid apical apparatus and ellipsoidal, dark ascospores with germ slits. Morphology and combined phylogenetic analysis of ITS, LSU, β-tubulin and RPB2 sequence data, showed it to be a new Rhopalostroma species introduced herein as R. brevistipitatum. A nodulisporium-like asexual morph was produced in culture. A morphological description and photographs of R. brevistipitatum are provided in this paper, with amendments to the generic description.

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TL;DR: A new genus Pseudosplanchnonema is introduced with P. phorcioides comb, isolated from dead branches of Acer campestre and Morus species, which formed a distinct clade within the family Massarinaceae and is sister to Massarina eburnea, the type species of Massarine.
Abstract: In this paper we introduce a new genus Pseudosplanchnonema with P. phorcioides comb. nov. , isolated from dead branches of Acer campestre and Morus species. The new genus is confirmed based on morphology and phylogenetic analyses of sequence data. Phylogenetic analyses based on combined LSU and SSU sequence data showed that P. phorcioides formed a distinct clade within the family Massarinaceae and is sister to Massarina eburnea, the type species of Massarina. The new genus Pseudosplanchnonema differs from Massarina in having ascomata without clypei, a thick peridium and larger, 1-septate, guttulate, dark brown ascospores. The new genus is compared with genera in the family Massarinaceae and a detailed description and illustrations of the species P. phorcioides, including its asexual morph, is provided.

Journal Article
01 Jan 2015-Sydowia
TL;DR: The taxonomy and phylogeny of the coelomycete genera Ciliochorella and Discosia which have appendaged conidia are examined in this article.
Abstract: The taxonomy and phylogeny of the coelomycete genera Ciliochorella and Discosia which have appendaged conidia are examined in this paper. The phylogeny of taxa in Amphisphaeriaceae is reconstructed based on analysis of large subunit (28S) ribosomal DNA (LSU) sequence data. This analysis confirms that Ciliochorella and Discosia are members of Amphisphaeriaceae (Xylariales). A combination of morphological characters together with analysis of the s-Tubulin (TUB) gene region can be used to distinguish species in Discosia. In addition Ciliochorella mangiferae and Discosia brasiliensis are characterized morphologically.

Journal Article
TL;DR: Maximum-likelihood and Bayesian analyses of combined ITS, LSU and SSU gene sequence data show that N. didymospora belongs in Didymosphaeriaceae, Pleosporales, and is compared with other morphologically and phylogenetically similar species.