Showing papers in "Fungal Diversity in 2020"
American Museum of Natural History1, University of Tartu2, University of Gothenburg3, Swedish University of Agricultural Sciences4, University of Oslo5, University of Hawaii at Manoa6, University of Copenhagen7, Purdue University8, Academy of Sciences of the Czech Republic9, University of Turin10, Harvard University11, Synlab Group12, Universidad Mayor13, Universidad Santo Tomás14, University of Electronic Science and Technology of China15, University of Warsaw16, Swedish Museum of Natural History17, Mae Fah Luang University18, University of Florida19, Laos Ministry of Agriculture and Forestry20, São Paulo Federal Institute of Education, Science and Technology21, Estonian University of Life Sciences22, Federal University of Pernambuco23, United States Department of Energy24, Del Rosario University25, National Autonomous University of Mexico26, Ghent University27, West Bengal State University28, Beijing Forestry University29, Pontifical Catholic University of Chile30, Chinese Academy of Sciences31, Field Museum of Natural History32, University of Potsdam33, Leibniz Association34, University of Gilan35, University of Alaska Fairbanks36, University of Tokyo37, University of Costa Rica38, Forest Research Institute39, University of Sydney40, Westmead Hospital41, Uppsala University42, Landcare Research43, University of Chittagong44, University of Memphis45, United Arab Emirates University46, Ministry of Land and Resources of the People's Republic of China47, University of Pretoria48, Royal Botanic Gardens49, Ocean University of China50, Guizhou University51, Mie University52, Hokkaido University53
TL;DR: Fungal traits and character database FungalTraits operating at genus and species hypothesis levels is presented in this article, which includes 17 lifestyle related traits of fungal and Stramenopila genera.
Abstract: The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
245 citations
Yunnan Agricultural University1, University of Mauritius2, Chiang Mai University3, King Saud University4, Mae Fah Luang University5, Helmholtz Centre for Environmental Research - UFZ6, Guizhou University7, Shenzhen University8, Chinese Academy of Sciences9, Dali University10, Thammasat University11, University of Electronic Science and Technology of China12, Kunming Institute of Botany13, World Agroforestry Centre14, Agharkar Research Institute15, Banaras Hindu University16, University of Delhi17, Pondicherry University18, Royal Botanic Gardens19, Federal University of Pernambuco20, University of Debrecen21, Royal Society22
TL;DR: The present study describes two new families, 12 new genera, 82 new species, five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports.
Abstract: Fungal diversity notes is one of the important journal series of fungal taxonomy that provide detailed descriptions and illustrations of new fungal taxa, as well as providing new information of fungal taxa worldwide. This article is the 11th contribution to the fungal diversity notes series, in which 126 taxa distributed in two phyla, six classes, 24 orders and 55 families are described and illustrated. Taxa in this study were mainly collected from Italy by Erio Camporesi and also collected from China, India and Thailand, as well as in some other European, North American and South American countries. Taxa described in the present study include two new families, 12 new genera, 82 new species, five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports. The two new families are Eriomycetaceae (Dothideomycetes, family incertae sedis) and Fasciatisporaceae (Xylariales, Sordariomycetes). The twelve new genera comprise Bhagirathimyces (Phaeosphaeriaceae), Camporesiomyces (Tubeufiaceae), Eriocamporesia (Cryphonectriaceae), Eriomyces (Eriomycetaceae), Neomonodictys (Pleurotheciaceae), Paraloratospora (Phaeosphaeriaceae), Paramonodictys (Parabambusicolaceae), Pseudoconlarium (Diaporthomycetidae, genus incertae sedis), Pseudomurilentithecium (Lentitheciaceae), Setoapiospora (Muyocopronaceae), Srinivasanomyces (Vibrisseaceae) and Xenoanthostomella (Xylariales, genera incertae sedis). The 82 new species comprise Acremonium chiangraiense, Adustochaete nivea, Angustimassarina camporesii, Bhagirathimyces himalayensis, Brunneoclavispora camporesii, Camarosporidiella camporesii, Camporesiomyces mali, Camposporium appendiculatum, Camposporium multiseptatum, Camposporium septatum, Canalisporium aquaticium, Clonostachys eriocamporesiana, Clonostachys eriocamporesii, Colletotrichum hederiicola, Coniochaeta vineae, Conioscypha verrucosa, Cortinarius ainsworthii, Cortinarius aurae, Cortinarius britannicus, Cortinarius heatherae, Cortinarius scoticus, Cortinarius subsaniosus, Cytospora fusispora, Cytospora rosigena, Diaporthe camporesii, Diaporthe nigra, Diatrypella yunnanensis, Dictyosporium muriformis, Didymella camporesii, Diutina bernali, Diutina sipiczkii, Eriocamporesia aurantia, Eriomyces heveae, Ernakulamia tanakae, Falciformispora uttaraditensis, Fasciatispora cocoes, Foliophoma camporesii, Fuscostagonospora camporesii, Helvella subtinta, Kalmusia erioi, Keissleriella camporesiana, Keissleriella camporesii, Lanspora cylindrospora, Loratospora arezzoensis, Mariannaea atlantica, Melanographium phoenicis, Montagnula camporesii, Neodidymelliopsis camporesii, Neokalmusia kunmingensis, Neoleptosporella camporesiana, Neomonodictys muriformis, Neomyrmecridium guizhouense, Neosetophoma camporesii, Paraloratospora camporesii, Paramonodictys solitarius, Periconia palmicola, Plenodomus triseptatus, Pseudocamarosporium camporesii, Pseudocercospora maetaengensis, Pseudochaetosphaeronema kunmingense, Pseudoconlarium punctiforme, Pseudodactylaria camporesiana, Pseudomurilentithecium camporesii, Pseudotetraploa rajmachiensis, Pseudotruncatella camporesii, Rhexocercosporidium senecionis, Rhytidhysteron camporesii, Rhytidhysteron erioi, Septoriella camporesii, Setoapiospora thailandica, Srinivasanomyces kangrensis, Tetraploa dwibahubeeja, Tetraploa pseudoaristata, Tetraploa thrayabahubeeja, Torula camporesii, Tremateia camporesii, Tremateia lamiacearum, Uzbekistanica pruni, Verruconis mangrovei, Wilcoxina verruculosa, Xenoanthostomella chromolaenae and Xenodidymella camporesii. The five new combinations are Camporesiomyces patagoniensis, Camporesiomyces vaccinia, Camposporium lycopodiellae, Paraloratospora gahniae and Rhexocercosporidium microsporum. The 22 new records on host and geographical distribution comprise Arthrinium marii, Ascochyta medicaginicola, Ascochyta pisi, Astrocystis bambusicola, Camposporium pellucidum, Dendryphiella phitsanulokensis, Diaporthe foeniculina, Didymella macrostoma, Diplodia mutila, Diplodia seriata, Heterosphaeria patella, Hysterobrevium constrictum, Neodidymelliopsis ranunculi, Neovaginatispora fuckelii, Nothophoma quercina, Occultibambusa bambusae, Phaeosphaeria chinensis, Pseudopestalotiopsis theae, Pyxine berteriana, Tetraploa sasicola, Torula gaodangensis and Wojnowiciella dactylidis. In addition, the sexual morphs of Dissoconium eucalypti and Phaeosphaeriopsis pseudoagavacearum are reported from Laurus nobilis and Yucca gloriosa in Italy, respectively. The holomorph of Diaporthe cynaroidis is also reported for the first time.
139 citations
University of Mauritius1, Mae Fah Luang University2, Kunming Institute of Botany3, Guizhou University4, University of Electronic Science and Technology of China5, Sultan Qaboos University6, Academy of Sciences of Uzbekistan7, Andijan State University8, King Saud University9, Royal Society10, Chiang Mai University11
TL;DR: Ten genera are examined as case studies to establish trends in fungal description and introduce new species in each genus to conclude whether the authors are anywhere near to flattening the curve in new species description.
Abstract: The recent realistic estimate of fungal numbers which used various algorithms was between 2.2 and 3.8 million. There are nearly 100,000 accepted species of Fungi and fungus-like taxa, which is between 2.6 and 4.5% of the estimated species. Several forums such as Botanica Marina series, Fungal Diversity notes, Fungal Biodiversity Profiles, Fungal Systematics and Evolution—New and Interesting Fungi, Mycosphere notes and Fungal Planet have enhanced the introduction of new taxa and nearly 2000 species have been introduced in these publications in the last decade. The need to define a fungal species more accurately has been recognized, but there is much research needed before this can be better clarified. We address the evidence that is needed to estimate the numbers of fungi and address the various advances that have been made towards its understanding. Some genera are barely known, whereas some plant pathogens comprise numerous species complexes and numbers are steadily increasing. In this paper, we examine ten genera as case studies to establish trends in fungal description and introduce new species in each genus. The genera are the ascomycetes Colletotrichum and Pestalotiopsis (with many species or complexes), Atrocalyx, Dothiora, Lignosphaeria, Okeanomyces, Rhamphoriopsis, Thozetella, Thyrostroma (relatively poorly studied genera) and the basidiomycete genus Lepiota. We provide examples where knowledge is incomplete or lacking and suggest areas needing further research. These include (1) the need to establish what is a species, (2) the need to establish how host-specific fungi are, not in highly disturbed urban areas, but in pristine or relatively undisturbed forests, and (3) the need to establish if species in different continents, islands, countries or regions are different, or if the same fungi occur worldwide? Finally, we conclude whether we are anywhere near to flattening the curve in new species description.
97 citations
TL;DR: Most fungal families found on Siam weed had divergence estimates with stem ages in the Cretaceous, which coincided with the expected origin of the host family (Asteraceae), which indicates that the species have jumped hosts, as it is unlikely that the taxa on the alien Siam Weed came from the Americas with its host.
Abstract: This article provides morphological descriptions and illustrations of microfungi associated with the invasive weed, Chromolaena odorata, which were mainly collected in northern Thailand. Seventy-seven taxa distributed in ten orders, 23 families (of which Neomassarinaceae is new), 12 new genera (Chromolaenicola, Chromolaenomyces, Longiappendispora, Pseudocapulatispora, Murichromolaenicola, Neoophiobolus, Paraleptospora, Pseudoroussoella, Pseudostaurosphaeria, Pseudothyridariella, Setoarthopyrenia, Xenoroussoella), 47 new species (Aplosporella chromolaenae, Arthrinium chromolaenae, Chromolaenicola chiangraiensis, C. lampangensis, C. nanensis, C. thailandensis, Chromolaenomyces appendiculatus, Diaporthe chromolaenae, Didymella chromolaenae, Dyfrolomyces chromolaenae, Leptospora chromolaenae, L. phraeana, Longiappendispora chromolaenae, Memnoniella chromolaenae, Montagnula chiangraiensis, M. chromolaenae, M. chromolaenicola, M. thailandica, Murichromolaenicola chiangraiensis, M. chromolaenae, Muyocopron chromolaenae, M. chromolaenicola, Neomassarina chromolaenae, Neoophiobolus chromolaenae, Neopyrenochaeta chiangraiensis, N. chromolaenae, N. thailandica, N. triseptatispora, Nigrograna chromolaenae, Nothophoma chromolaenae, Paraleptospora chromolaenae, P. chromolaenicola, Patellaria chromolaenae, Pseudocapulatispora longiappendiculata, Pseudoroussoella chromolaenae, Pseudostaurosphaeria chromolaenae, P. chromolaenicola, Pseudothyridariella chromolaenae, Pyrenochaetopsis chromolaenae, Rhytidhysteron chromolaenae, Setoarthopyrenia chromolaenae, Sphaeropsis chromolaenicola, Tremateia chiangraiensis, T. chromolaenae, T. thailandensis, Xenoroussoella triseptata, Yunnanensis chromolaenae), 12 new host records, three new taxonomic combinations (Chromolaenicola siamensis, Pseudoroussoella elaeicola, Pseudothyridariella mahakashae), and two reference specimens (Torula chromolaenae, T. fici) are described and illustrated. Unlike some other hosts, e.g. bamboo (Poaceae) and Pandanaceae, the dominant group of fungi on Siam weed were Dothideomycetes. Only 15 species previously recorded from northern Thailand were found in this study. Most of the taxa are likely to have jumped hosts from surrounding plants and are unlikely to be a specialist to Siam weed. Most fungal families found on Siam weed had divergence estimates with stem ages in the Cretaceous, which coincided with the expected origin of the host family (Asteraceae). This further indicates that the species have jumped hosts, as it is unlikely that the taxa on the alien Siam weed came from the Americas with its host. They may, however, have jumped from other Asteraceae hosts. In a preliminary screening 40 (65%) of the 62 species tested showed antimicrobial activity and thus, the fungi associated with C. odorata may be promising sources of novel bioactive compound discovery. We provide a checklist of fungi associated with C. odorata based on the USDA Systematic Mycology and Microbiology Laboratory (SMML) database, relevant literature and our study. In total, 130 taxa (116 identified and 14 unidentified species) are distributed in 20 orders, 48 families, and 85 genera. Pseudocercospora is the most commonly encountered genus on Siam weed.
83 citations
TL;DR: The study revealed two new families, 12 new genera, 50 new species, 26 new host records with one dimorphic character report, and ten species are transferred to other genera on Clematis.
Abstract: The cosmopolitan plant genus Clematis contains many climbing species that can be found worldwide. The genus occurs in the wild and is grown commercially for horticulture. Microfungi on Clematis were collected from Belgium, China, Italy, Thailand and the UK. They are characterized by morphology and analyses of gene sequence data using an integrated species concept to validate identifications. The study revealed two new families, 12 new genera, 50 new species, 26 new host records with one dimorphic character report, and ten species are transferred to other genera. The new families revealed by multigene phylogeny are Longiostiolaceae and Pseudomassarinaceae in Pleosporales (Dothideomycetes). New genera are Anthodidymella (Didymellaceae), Anthosulcatispora and Parasulcatispora (Sulcatisporaceae), Fusiformispora (Amniculicolaceae), Longispora (Phaeosphaeriaceae), Neobyssosphaeria (Melanommataceae), Neoleptosporella (Chaetosphaeriales, genera incertae sedis), Neostictis (Stictidaceae), Pseudohelminthosporium (Neomassarinaceae), Pseudomassarina (Pseudomassarinaceae), Sclerenchymomyces (Leptosphaeriaceae) and Xenoplectosphaerella (Plectosphaerellaceae). The newly described species are Alloleptosphaeria clematidis, Anthodidymella ranunculacearum, Anthosulcatispora subglobosa, Aquadictyospora clematidis, Brunneofusispora clematidis, Chaetosphaeronema clematidicola, C. clematidis, Chromolaenicola clematidis, Diaporthe clematidina, Dictyocheirospora clematidis, Distoseptispora clematidis, Floricola clematidis, Fusiformispora clematidis, Hermatomyces clematidis, Leptospora clematidis, Longispora clematidis, Massariosphaeria clematidis, Melomastia clematidis, M. fulvicomae, Neobyssosphaeria clematidis, Neoleptosporella clematidis, Neoroussoella clematidis, N. fulvicomae, Neostictis nigricans, Neovaginatispora clematidis, Parasulcatispora clematidis, Parathyridaria clematidis, P. serratifoliae, P. virginianae, Periconia verrucose, Phomatospora uniseriata, Pleopunctum clematidis, Pseudocapulatispora clematidis, Pseudocoleophoma clematidis, Pseudohelminthosporium clematidis, Pseudolophiostoma chiangraiense, P. clematidis, Pseudomassarina clematidis, Ramusculicola clematidis, Sarocladium clematidis, Sclerenchymomyces clematidis, Sigarispora clematidicola, S. clematidis, S. montanae, Sordaria clematidis, Stemphylium clematidis, Wojnowiciella clematidis, Xenodidymella clematidis, Xenomassariosphaeria clematidis and Xenoplectosphaerella clematidis. The following fungi are recorded on Clematis species for the first time: Angustimassarina rosarum, Dendryphion europaeum, Dermatiopleospora mariae, Diaporthe ravennica, D. rudis, Dichotomopilus ramosissimum, Dictyocheirospora xishuangbannaensis, Didymosphaeria rubi-ulmifolii, Fitzroyomyces cyperacearum, Fusarium celtidicola, Leptospora thailandica, Memnoniella oblongispora, Neodidymelliopsis longicolla, Neoeutypella baoshanensis, Neoroussoella heveae, Nigrograna chromolaenae, N. obliqua, Pestalotiopsis verruculosa, Pseudoberkleasmium chiangmaiense, Pseudoophiobolus rosae, Pseudoroussoella chromolaenae, P. elaeicola, Ramusculicola thailandica, Stemphylium vesicarium and Torula chromolaenae. The new combinations are Anthodidymella clematidis (≡ Didymella clematidis), A. vitalbina (≡ Didymella vitalbina), Anthosulcatispora brunnea (≡ Neobambusicola brunnea), Fuscohypha kunmingensis (≡ Plectosphaerella kunmingensis), Magnibotryascoma rubriostiolata (≡ Teichospora rubriostiolata), Pararoussoella mangrovei (≡ Roussoella mangrovei), Pseudoneoconiothyrium euonymi (≡ Roussoella euonymi), Sclerenchymomyces jonesii (≡ Neoleptosphaeria jonesii), Stemphylium rosae (≡ Pleospora rosae), and S. rosae-caninae (≡ Pleospora rosae-caninae). The microfungi on Clematis is distributed in several classes of Ascomycota. The analyses are based on morphological examination of specimens, coupled with phylogenetic sequence data. To the best of our knowledge, the consolidated species concept approach is recommended in validating species.
77 citations
Shenzhen University1, Chiang Mai University2, Mae Fah Luang University3, Zhongkai University of Agriculture and Engineering4, Kunming Institute of Botany5, Landcare Research6, Pondicherry University7, Free University of Berlin8, Virginia Tech College of Natural Resources and Environment9, Chinese Academy of Sciences10, King Saud University11, University of Lisbon12, National Chiayi University13, University of Mauritius14, Guizhou University15, University of Electronic Science and Technology of China16, Dali University17, University of Sri Jayewardenepura18, Botanic Garden Meise19, Spanish National Research Council20, University of Tartu21, Rajiv Gandhi University of Health Sciences22, National Taiwan University23, Kunming University of Science and Technology24, Universidade Federal de Goiás25, Oregon State University26, Federal University of Mato Grosso do Sul27, University of Liège28, Commonwealth Scientific and Industrial Research Organisation29, Thailand National Science and Technology Development Agency30
TL;DR: A refined updated document on orders and families incertae sedis of Dothideomycetes is provided, including an updated description, notes, including figures to represent the morphology, a list of accepted genera, and economic and ecological significances and phylogenetic trees for each order.
Abstract: Numerous new taxa and classifications of Dothideomycetes have been published following the last monograph of families of Dothideomycetes in 2013. A recent publication by Honsanan et al. in 2020 expanded information of families in Dothideomycetidae and Pleosporomycetidae with modern classifications. In this paper, we provide a refined updated document on orders and families incertae sedis of Dothideomycetes. Each family is provided with an updated description, notes, including figures to represent the morphology, a list of accepted genera, and economic and ecological significances. We also provide phylogenetic trees for each order. In this study, 31 orders which consist 50 families are assigned as orders incertae sedis in Dothideomycetes, and 41 families are treated as families incertae sedis due to lack of molecular or morphological evidence. The new order, Catinellales, and four new families, Catinellaceae, Morenoinaceae Neobuelliellaceae and Thyrinulaceae are introduced. Seven genera (Neobuelliella, Pseudomicrothyrium, Flagellostrigula, Swinscowia, Macroconstrictolumina, Pseudobogoriella, and Schummia) are introduced. Seven new species (Acrospermum urticae, Bogoriella complexoluminata, Dothiorella ostryae, Dyfrolomyces distoseptatus, Macroconstrictolumina megalateralis, Patellaria microspora, and Pseudomicrothyrium thailandicum) are introduced base on morphology and phylogeny, together with two new records/reports and five new collections from different families. Ninety new combinations are also provided in this paper.
59 citations
TL;DR: The present study revises the classification of the hyaline-spored coelomycetes and provides a modern taxonomic framework based on both morphology and phylogeny.
Abstract: Coelomycete is a general term used for asexual fungi which produce conidia in fruiting bodies: pycnidial, acervular, cupulate, pycnothyria or stromatic conidiomata. The group contains numerous plant pathogenic, saprobic and endophytic species associated with a wide range of hosts. Traditionally, morphological characters and host associations have been used as criteria to identify and classify coelomycetes, and this has resulted in a poor understanding of their generic and species boundaries. DNA based taxonomic studies have provided a better outlook of the phylogenetic and evolutionary trends in coelomycetes. However, the present outcomes represent only a preliminary step towards the understanding of coelomycetes. Many genera have not been revisited since they were first described. The present study revises the classification of the hyaline-spored coelomycetes and provides a modern taxonomic framework based on both morphology and phylogeny. In total, 248 genera were investigated, of which less than 100 are known to have sequence data. Multi-locus sequence data analyses of 28S nrDNA, 18S nrDNA, ITS, RNA polymerase II second largest subunit (rpb2), and part of the translation elongation factor 1-alpha gene (tef1) and β-tubulin (tub2) gene regions were analysed. As a result, three new genera and 23 new species are introduced. In addition, three new links between sexual and asexual genera are provided. There are 138 genera that lack sequence data, and these are treated as Ascomycota, genera incertae sedis. Line drawings and descriptions are provided based on the examination of types and fresh collections and on the literature.
58 citations
TL;DR: In this article, the phylogenetic placement of previously unrecognized fungal groups was addressed by using two complementary approaches: (i) third-generation amplicon sequencing analysis of DNA from global soil samples, screening out ITS reads of ≥ 90% similarity to other available Sanger sequences, and (ii) analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone (so-called top50 sequences).
Abstract: Molecular identification methods, in particular high-throughput sequencing tools, have greatly improved our knowledge about fungal diversity and biogeography, but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic levels. This study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches: (i) third-generation amplicon sequencing analysis of DNA from global soil samples, screening out ITS reads of < 90% similarity to other available Sanger sequences, and (ii) analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone (so-called top50 sequences). For the global soil samples, we chose to amplify the full rRNA gene operon using four partly overlapping amplicons and multiple newly developed primers or primer combinations that cover nearly all fungi and a vast majority of non-fungal eukaryotes. We extracted the rRNA 18S (SSU) and 28S (LSU) genes and performed phylogenetic analyses against carefully selected reference material. Both SSU and LSU analyses placed most soil sequences and top50 sequences to known orders and classes, but tens of monophyletic groups and single sequences remained outside described taxa. Furthermore, the LSU analyses recovered a few small groups of sequences that may potentially represent novel phyla. We conclude that rRNA genes-based phylogenetic analyses are efficient tools for determining phylogenetic relationships of fungal taxa that cannot be placed to any order or class using ITS sequences alone. However, in many instances, longer rRNA gene sequences and availability of both SSU and LSU reads are needed to improve taxonomic resolution. By leveraging third-generation sequencing from global soil samples, we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life, with 10–20% new order-level taxa. In addition, the PacBio sequence data greatly extends fungal class-level information in reference databases.
44 citations
TL;DR: This work applies two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics, leading to a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset.
Abstract: Early efforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic groups led to the definition of 14 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a well-resolved phylogeny. The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach, but was unable to resolve higher-level organization of groups. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity, biology, and evolution.
43 citations
TL;DR: A new phylogenetic framework of Cordycipitaceae is reconstructed using multigene sequence data with large-scale taxon sampling to determine their phylogenetic placements and two new genera (Flavocillium and Liangia), 16 new species and four new combinations are introduced.
Abstract: The phylogeny and systematics of cordycipitoid fungi have been extensively studied in the last two decades. However, systematic positions of some taxa in the family Cordycipitaceae have not yet been thoroughly resolved. In this study, a new phylogenetic framework of Cordycipitaceae is reconstructed using multigene (nrSSU, nrLSU, tef-1α, rpb1 and rpb2) sequence data with large-scale taxon sampling. In addition, ITS sequence data of species belonging to the Lecanicillium lineage in the family Cordycipitaceae are used to further determine their phylogenetic placements. Based on molecular phylogenetic data together with morphological evidence, two new genera (Flavocillium and Liangia), 16 new species and four new combinations are introduced. In the new genus Flavocillium, one new species F. bifurcatum and three new combinations previously described as Lecanicillium, namely F. acerosium, F. primulinium and F. subprimulinium, are proposed. The genus Liangia is built by the new species Lia. sinensis with Lecanicillium-like asexual morph, isolated from an entomopathogenic fungus Beauveria yunnanensis. Due to the absence of Paecilomyces hepiali, an economically and medically significant fungus, in the earlier phylogenetic analyses, its systematic position has been puzzling in both business and academic communities for a long time. Here, P. hepiali is recharacterized using the holotype material along with seven additional samples. It is assigned to the genus Samsoniella (Cordycipitaceae, Hypocreales) possessing Cordyceps-like sexual morph and Isaria-like asexual morph, and thus a new combination, namely S. hepiali is proposed. An additional nine new species in Samsoniella are described: S. alpina, S. antleroides, S. cardinalis, S. cristata, S. lanmaoa, S. kunmingensis, S. ramosa, S. tortricidae and S. yunnanensis. Four new species in Cordyceps are described: C. chaetoclavata, C. cocoonihabita, C. shuifuensis and C. subtenuipes. Simplicillium yunnanense, isolated from synnemata of Akanthomyces waltergamsii, is described as a new species.
40 citations
TL;DR: The phylogeny shows that Muscodor species have affinities to the xylarialean genera Emarcea and Induratia, which is corroborated by the fact that their sexual states produce characteristic apiospores, which allow for the integration of Mus codor in Induratian, i.e. the genus that was historically described first.
Abstract: Molecular phylogenetic studies of cultures derived from some specimens of plant-inhabiting Sordariomycetes using ITS, LSU, rpb2 and tub2 DNA sequence data revealed close affinities to strains of Muscodor. The taxonomy of this biotechnologically important genus, which exclusively consists of endophytes with sterile mycelia that produce antibiotic volatile secondary metabolites, was based on a rather tentative taxonomic concept. Even though it was accommodated in Xylariaceae, its phylogenetic position had so far remained obscure. Our phylogeny shows that Muscodor species have affinities to the xylarialean genera Emarcea and Induratia, which is corroborated by the fact that their sexual states produce characteristic apiospores. These data allow for the integration of Muscodor in Induratia, i.e. the genus that was historically described first. The multi-locus phylogenetic tree clearly revealed that a clade comprising Emarcea and Induratia forms a monophylum separate from representatives of Xylariaceae, for which we propose the new family Induratiaceae. Divergence time estimations revealed that Induratiaceae has been diverged from the Xylariaceae + Clypeosphaeriaceae clade at 93 (69–119) million years ago (Mya) with the crown age of 61 (39–85) Mya during the Cretaceous period. The ascospore-derived cultures were studied for the production of volatile metabolites, using both, dual cultures for assessment of antimicrobial effects and extensive analyses using gas chromatography coupled with mass spectrometry (GC–MS). The antimicrobial effects observed were significant, but not as strong as in the case of the previous reports on Muscodor species. The GC–MS results give rise to some doubt on the validity of the previous identification of certain volatiles. Many peaks in the GC–MS chromatograms could not be safely identified by database searches and may represent new natural products. The isolation of these compounds by preparative chromatography and their subsequent characterisation by nuclear magnetic resonance (NMR) spectroscopy or total synthesis will allow for a more concise identification of these volatiles, and they should also be checked for their individual contribution to the observed antibiotic effects. This will be an important prerequisite for the development of biocontrol strains.
TL;DR: The efficiency of different DNA barcodes in species delimitation in Bipolaris is evaluated by phylogenetic analyses, Automatic Barcode Gap Discovery and Objective Clustering, and GAPDH is determined to be the best single marker for the genus.
Abstract: Bipolaris species are important plant pathogens with a worldwide distribution in tropical and temperate environments. Species recognition in Bipolaris has been problematic due to a lack of molecular data from ex-type cultures, the use of few gene regions for species resolution and overlapping morphological characters. In this study, we evaluate the efficiency of different DNA barcodes in species delimitation in Bipolaris by phylogenetic analyses, Automatic Barcode Gap Discovery and Objective Clustering. GAPDH is determined to be the best single marker for the genus. These approaches are used to clarify the taxonomic placement of all sequences currently named as Bipolaris in GenBank based on ITS and GAPDH gene sequence data. In checking various publications, we found that the majority of new host records of fungal species published in the Plant Disease journal from 2010 to 2019 were based on BLAST searches of the ITS sequences and up to 82% of those records could be erroneous. Therefore, relying on BLAST searches from GenBank to name species is not recommended. Editorial boards of journals and reviewers of new record papers should be aware of this problem. In naming Bipolaris species, whether new or known, it is recommended to perform phylogenetic analyses based on GAPDH using the correct taxon sampling for accurate results and the species relationship should have reliable statistical support. At least two new species are represented by molecular data in GenBank and we provide an updated taxonomic revision of Bipolaris. We accept 45 species in Bipolaris and notes are provided for all the species including hosts and geographic distribution.
TL;DR: The dataset is unbalanced in that a large part of the extant biodiversity has not been analyzed by molecular methods, novel taxonomic entities being introduced at a regular pace.
Abstract: Chaetothyriales is an ascomycetous order within Eurotiomycetes. The order is particularly known through the black yeasts and filamentous relatives that cause opportunistic infections in humans. All species in the order are consistently melanized. Ecology and habitats of species are highly diverse, and often rather extreme in terms of exposition and toxicity. Families are defined on the basis of evolutionary history, which is reconstructed by time of divergence and concepts of comparative biology using stochastical character mapping and a multi-rate Brownian motion model to reconstruct ecological ancestral character states. Ancestry is hypothesized to be with a rock-inhabiting life style. Ecological disparity increased significantly in late Jurassic, probably due to expansion of cytochromes followed by colonization of vacant ecospaces. Dramatic diversification took place subsequently, but at a low level of innovation resulting in strong niche conservatism for extant taxa. Families are ecologically different in degrees of specialization. One of the clades has adapted ant domatia, which are rich in hydrocarbons. In derived families, similar processes have enabled survival in domesticated environments rich in creosote and toxic hydrocarbons, and this ability might also explain the pronounced infectious ability of vertebrate hosts observed in these families. Conventional systems of morphological classification poorly correspond with recent phylogenetic data. Species are hypothesized to have low competitive ability against neighboring microbes, which interferes with their laboratory isolation on routine media. The dataset is unbalanced in that a large part of the extant biodiversity has not been analyzed by molecular methods, novel taxonomic entities being introduced at a regular pace. Our study comprises all available species sequenced to date for LSU and ITS, and a nomenclatural overview is provided. A limited number of species could not be assigned to any extant family.
TL;DR: The need to follow polyphasic approach in species delimitation of Trichophyton benhamiae pathogens is demonstrated, due to considerable phenotypic similarity of many dermatophytes and phenomena such as incomplete lineage sorting or occasional hybridization and introgression.
Abstract: Species of the Trichophyton benhamiae complex are predominantly zoophilic pathogens with a worldwide distribution. These pathogens have recently become important due to their epidemic spread in pets and pet owners. Considerable genetic and phenotypic variability has been revealed in these emerging pathogens, but the species limits and host spectra have not been clearly elucidated. In this study, we used an approach combining phylogenetic analysis based on four loci, population-genetic data, phenotypic and physiological analysis, mating type gene characterization and ecological data to resolve the taxonomy of these pathogens. This approach supported the inclusion of nine taxa in the complex, including three new species and one new variety. Trichophyton benhamiae var. luteum var. nov. (“yellow phenotype” strains) is currently a major cause of zoonotic tinea corporis and capitis in Europe (mostly transmitted from guinea pigs). The isolates of the “white phenotype” do not form a monophyletic group and are segregated into three taxa, T. benhamiae var. benhamiae (mostly North America; dogs), T. europaeum sp. nov. (mostly Europe; guinea pigs), and T. japonicum sp. nov. (predominant in East Asia but also found in Europe; rabbits and guinea pigs). The new species T. africanum sp. nov. is proposed for the “African” race of T. benhamiae. The introduction to new geographic areas and host jump followed by extinction of one mating type gene have played important roles in the evolution of these pathogens. Due to considerable phenotypic similarity of many dermatophytes and phenomena such as incomplete lineage sorting or occasional hybridization and introgression, we demonstrate the need to follow polyphasic approach in species delimitation. Neutrally evolving and noncoding DNA regions showed significantly higher discriminatory power compared to conventional protein-coding loci. Diagnostic options for species identification in practice based on molecular markers, phenotype and MALDI-TOF spectra are presented. A microsatellite typing scheme developed in this study is a powerful tool for the epidemiological surveillance of these emerging pathogens.
TL;DR: This study shows that nomenclatural problems, even in difficult groups like C. subgenus Telamonia, can be solved and consequently identification of species based on ITS barcodes becomes an easy task even for non-experts of the genus.
Abstract: So far approximately 144,000 species of fungi have been named but sequences of the majority of them do not exist in the public databases. Therefore, the quality and coverage of public barcode databases is a bottleneck that hinders the study of fungi. Cortinarius is the largest genus of Agaricales with thousands of species world-wide. The most diverse subgenus in Cortinarius is Telamonia and its species have been considered one of the most taxonomically challenging in the Agaricales. Its high diversity combined with convergent, similar appearing taxa have earned it a reputation of being an impossible group to study. In this study a total of 746 specimens, including 482 type specimens representing 184 species were sequenced. Also, a significant number of old types were successfully sequenced, 105 type specimens were over 50 years old and 18 type specimens over 100 years old. Altogether, 20 epi- or neotypes are proposed for recently commonly used older names. Our study doubles the number of reliable DNA-barcodes of species of C. subgenus Telamonia in the public sequence databases. This is also the first extensive phylogenetic study of the subgenus. A majority of the sections and species are shown in a phylogenetic context for the first time. Our study shows that nomenclatural problems, even in difficult groups like C. subgenus Telamonia, can be solved and consequently identification of species based on ITS barcodes becomes an easy task even for non-experts of the genus.
TL;DR: Ancestral character state analysis within a broader context of Arthoniales does not support the saprotrophic lifestyle to be a plesiomorphic feature, but suggests loss of lichenization in Naevia, as well as loss and possible regain in a second clade containing saprotroph species and including taxa resembling Mycoporum, underlining the evolutionary plasticity of Arstoniales.
Abstract: Fungi that are barely lichenized or non-lichenized and closely related to lichenized taxa, the so-called borderline fungi, are an important element in reconstructing the evolutionary history of lichenized lineages. Arthoniaceae is a prime example including non-lichenized, saprotrophic lineages which potentially were precursors to lichenized taxa. In this study, we focused on saprotrophic species of Arthonia sensu lato, including new sequence data for Arthonia pinastri. We obtained fresh material of this taxon from a living branch of Fraxinus ornus in Italy to assess its taxonomic status and to elucidate its phylogenetic relationships within Arthonia. Thin sections of the thallus and ascomata of A. pinastri confirmed the absence of a photobiont. Maximum likelihood and Bayesian analyses of combined mtSSU, nuLSU and RPB2 sequence data placed the species close to A. dispersa (barely lichenized or non-lichenized) and A. punctiformis (non-lichenized) in a clade closely related to Arthonia sensu stricto, and the A. pinastri clade is here resurrected under the name Naevia. Ancestral character state analysis within a broader context of Arthoniales does not support the saprotrophic lifestyle to be a plesiomorphic feature, but suggests loss of lichenization in Naevia, as well as loss and possible regain in a second clade containing saprotrophic species and including taxa resembling Mycoporum, underlining the evolutionary plasticity of Arthoniales. These two clades constitute model taxa to further investigate the evolution of alternative biological lifestyles within the context of chiefly lichenized taxa.
TL;DR: Phylogenetic inference of the Tricholomatineae based on the analysis of a combined dataset of nuclear genes supports significantly a monophyletic origin of the aforementioned genera with the exception of Catathelasma, which is significantly related with Bonomyces and Cleistocybe.
Abstract: A new classification of the taxa formerly ascribed to Biannulariaceae (≡ Catathelasmataceae), viz. Catathelasma (type), Callistosporium, Pleurocollybia, Macrocybe, Pseudolaccaria, Guyanagarika and Anupama is here proposed. Phylogenetic inference of the Tricholomatineae based on the analysis of a combined dataset of nuclear genes including ITS, 18S and 28S rDNA, tef1 and rpb2 data supports significantly a monophyletic origin of the aforementioned genera with the exception of Catathelasma, which is significantly related with Bonomyces and Cleistocybe. Biannulariaceae is therefore emended to include the clade formed by Catathelasma, Bonomyces and Cleistocybe. Consequently, the new family Callistosporiaceae is proposed to name the clade containing Callistosporium (= Pleurocollybia) and related genera. Species of Callistosporium with distant lamellae, long hygrophoroid basidia and large amygdaliform spores are accommodated in the new genus Xerophorus. Finally, the new species Callistosporium pseudofelleum and Macrocybe sardoa are described, Clitocybe hesleri and C. fellea are combined into Callistosporium and Pseudolaccaria, respectively, and Callistosporium olivascens var. donadinii is upgraded to species rank and combined into Xerophorus.
TL;DR: It is shown that foliicolous species form six well-delimited clades that correlate with diagnostic phenotype features, including thallus morphology, carbonization of the involucrellum and excipulum, ascospore dimensions, and type of macroconidia, in Strigula sensu lato.
Abstract: Strigula sensu lato has been previously defined based on phenotype characters as a rather broad genus including tropical to temperate species growing on a wide array of substrata. In this study, based on a multilocus phylogenetic approach, we show that foliicolous species form six well-delimited clades that correlate with diagnostic phenotype features, including thallus morphology, carbonization of the involucrellum and excipulum, ascospore dimensions, and type of macroconidia. Given the topology, with five of the six clades emerging on long stem branches, and the strong phenotypical differentiation between the clades, we recognize these at the genus level, making mostly use of previously established genus names. Four genera, namely Phylloporis, Puiggariella, Raciborskiella, and Racoplaca, are resurrected for the S. phyllogena, S. nemathora, S. janeirensis, and S. subtilissima groups, respectively, whereas one new genus, Serusiauxiella gen. nov., is introduced for a novel lineage with peculiar macroconidia. The only sequenced non-foliicolous species, S. jamesii, is not closely related to these six foliicolous lineages but clusters with Flavobathelium and Phyllobathelium, revealing it as an additional undescribed genus-level lineage being treated elsewhere. Within the new genus Serusiauxiella, three new species are described: Serusiauxiella filifera sp. nov., S. flagellata sp. nov., and S. sinensis sp. nov. In addition, ten new combinations are proposed: Phylloporis austropunctata comb. nov., P. radiata comb. nov., P. vulgaris comb. nov., Puiggariella confluens comb. et stat. nov., P. nemathora comb. nov., P. nigrocincta comb. nov., Racoplaca maculata comb. nov., R. melanobapha comb. nov., R. transversoundulata, and R. tremens comb. nov. We also report on a peculiar, previously unrecognized growth behaviour of the macroconidial appendages in Strigula s.lat.
TL;DR: A special issue of Fungal Diversity is published in honour of Erio Camporesi, who has promoted mycological research as a prodigious amateur mycologist and collector of fungi.
Abstract: We are proud to publish a special issue of Fungal Diversity in honour of the contributions made by Erio Camporesi, who has promoted mycological research as a prodigious amateur mycologist and collector of fungi. The special issue includes Fungal Diversity notes 11, with many taxa named in Erio’s honour and a monograph of hyaline-spored Coelomycetes, both incorporating many of Erio’s collections. Erio obtained a certificate of accountancy in 1982 and worked as an accountant at the express courier company, TNT Global Express SPA. He was always interested in collecting microfungi, mushrooms and toadstools and in doing so this passion has occupied much of his spare time. His first collection in 1984 was of a mushroom, Suillellus luridus (: Boletus luridus). Erio was particularly interested in microfungi associated with plants. He started to collaborate with Kevin D. Hyde through the AscoFrance website (http://www.ascofrance.com). The first fungal specimen to be loaned to Kevin D. Hyde was Dothidella ulmi. Since then, Erio has sent thousands of herbarium specimens for study. Erio’s mother, Maria Ghetti, who accompanied Erio on many forays (Fig. 1), died on 21 April 2012 leaving Erio to care for his aging father, Nello Camporesi, who also accompanied Erio on forays and died on 24 February 2019 (Fig. 1). Erio retired from his permanent accounting job in 2013 and, thereafter, his interest in mycology became a top priority. He also had a talent for painting and many of his paintings incorporated fungi in imaginative ways (Fig. 2). Italian mycology has an exceptional history with the early contributions by Giuseppe De Notaris (1805–1877), Vincenzo de Cesati (1806–1883) and Pier Andrea Saccardo (1845–1920) who greatly contributed to the fungal