Studies in Mycology最新文献

{"title":"Lessons on fruiting body morphogenesis from genomes and transcriptomes of <i>Agaricomycetes</i>.","authors":"L G Nagy,&nbsp;P J Vonk,&nbsp;M Künzler,&nbsp;C Földi,&nbsp;M Virágh,&nbsp;R A Ohm,&nbsp;F Hennicke,&nbsp;B Bálint,&nbsp;Á Csernetics,&nbsp;B Hegedüs,&nbsp;Z Hou,&nbsp;X B Liu,&nbsp;S Nan,&nbsp;M Pareek,&nbsp;N Sahu,&nbsp;B Szathmári,&nbsp;T Varga,&nbsp;H Wu,&nbsp;X Yang,&nbsp;Z Merényi","doi":"10.3114/sim.2022.104.01","DOIUrl":"https://doi.org/10.3114/sim.2022.104.01","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (&lt;i&gt;Agaricomycetes&lt;/i&gt;) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of &lt;i&gt;Coprinopsis cinerea&lt;/i&gt;, and their orthologs in &lt;i&gt;Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus&lt;/i&gt;, and &lt;i&gt;Schizophyllum commune&lt;/i&gt;, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the &lt;i&gt;Agaricomycetes&lt;/i&gt;. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. &lt;b&gt;Citation:&lt;/b&gt; Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of &lt;i&gt;Agaricomycetes. Studies in Mycology&lt;/i&gt; &lt;b&gt;104&lt;/b&gt;: 1-85. doi: 10","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"104 ","pages":"1-85"},"PeriodicalIF":16.5,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10282164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9713175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A genome-informed higher rank classification of the biotechnologically important fungal subphylum <i>Saccharomycotina</i>.","authors":"M Groenewald, C T Hittinger, K Bensch, D A Opulente, X-X Shen, Y Li, C Liu, A L LaBella, X Zhou, S Limtong, S Jindamorakot, P Gonçalves, V Robert, K H Wolfe, C A Rosa, T Boekhout, N Čadež, G Éter, J P Sampaio, M-A Lachance, A M Yurkov, H-M Daniel, M Takashima, K Boundy-Mills, D Libkind, K Aoki, T Sugita, A Rokas","doi":"10.3114/sim.2023.105.01","DOIUrl":"10.3114/sim.2023.105.01","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The subphylum &lt;i&gt;Saccharomycotina&lt;/i&gt; is a lineage in the fungal phylum &lt;i&gt;Ascomycota&lt;/i&gt; that exhibits levels of genomic diversity similar to those of plants and animals. The &lt;i&gt;Saccharomycotina&lt;/i&gt; consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum &lt;i&gt;Saccharomycotina&lt;/i&gt; has much higher rates of genome sequence evolution than its sister subphylum, &lt;i&gt;Pezizomycotina&lt;/i&gt;, it contains only one class compared to the 16 classes in &lt;i&gt;Pezizomycotina&lt;/i&gt;. The third subphylum of &lt;i&gt;Ascomycota&lt;/i&gt;, the &lt;i&gt;Taphrinomycotina&lt;/i&gt;, consists of six classes and has approximately 10 times fewer species than the &lt;i&gt;Saccharomycotina&lt;/i&gt;. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the &lt;i&gt;Saccharomycotina&lt;/i&gt; contains 12 major and robustly supported phylogenetic clades; seven of these are current families (&lt;i&gt;Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae&lt;/i&gt;, and &lt;i&gt;Saccharomycetaceae&lt;/i&gt;), one comprises two current families (&lt;i&gt;Dipodascaceae&lt;/i&gt; and &lt;i&gt;Trichomonascaceae&lt;/i&gt;), one represents the genus &lt;i&gt;Sporopachydermia&lt;/i&gt;, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the &lt;i&gt;Saccharomycotina&lt;/i&gt;, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the &lt;i&gt;Saccharomycotina&lt;/i&gt; more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. &lt;b&gt;Taxonomic novelties: New classes:&lt;/b&gt; &lt;i&gt;Alloascoideomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas, &lt;i&gt;Dipodascomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas, &lt;i&gt;Lipomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente, A. Rokas, &lt;i&gt;Pichiomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas, &lt;i&gt;Sporopachydermiomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas, &lt;i&gt;Trigonopsidomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas. &lt;b&gt;New orders:&lt;/b&gt; &lt;i&gt;&lt;b&gt;Alloascoideomycetes:&lt;/b&gt;&lt;/i&gt; &lt;i&gt;Alloascoideales&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas; &lt;i&gt;&lt;b&gt;Di","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"1 1","pages":"1-22"},"PeriodicalIF":14.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11182611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69600543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revising <i>Clonostachys</i> and allied genera in <i>Bionectriaceae</i>.","authors":"L Zhao, J Z Groenewald, M Hernández-Restrepo, H-J Schroers, P W Crous","doi":"10.3114/sim.2023.105.03","DOIUrl":"10.3114/sim.2023.105.03","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Clonostachys&lt;/i&gt; (&lt;i&gt;Bionectriaceae&lt;/i&gt;, &lt;i&gt;Hypocreales&lt;/i&gt;) species are common soil-borne fungi, endophytes, epiphytes, and saprotrophs. Sexual morphs of &lt;i&gt;Clonostachys&lt;/i&gt; spp&lt;i&gt;.&lt;/i&gt; were placed in the genus &lt;i&gt;Bionectria&lt;/i&gt;, which was further segregated into the six subgenera &lt;i&gt;Astromata&lt;/i&gt;, &lt;i&gt;Bionectria&lt;/i&gt;, &lt;i&gt;Epiphloea&lt;/i&gt;, &lt;i&gt;Myronectria&lt;/i&gt;, &lt;i&gt;Uniparietina&lt;/i&gt;, and &lt;i&gt;Zebrinella&lt;/i&gt;. However, with the end of dual nomenclature, &lt;i&gt;Clonostachys&lt;/i&gt; became the single depository for sexual and asexual morph-typified species. Species of &lt;i&gt;Clonostachys&lt;/i&gt; are typically characterised by penicillate, sporodochial, and, in many cases, dimorphic conidiophores (primary and secondary conidiophores). Primary conidiophores are mononematous, either verticillium-like or narrowly penicillate. The secondary conidiophores generally form imbricate conidial chains that can collapse to slimy masses, particularly on sporodochia. In the present study, we investigated the species diversity within a collection of 420 strains of &lt;i&gt;Clonostachys&lt;/i&gt; from the culture collection of, and personal collections at, the Westerdijk Fungal Biodiversity Institute in Utrecht, the Netherlands. Strains were analysed based on their morphological characters and molecular phylogeny. The latter used DNA sequence data of the nuclear ribosomal internal transcribed spacer regions and intervening 5.8S nrDNA (ITS) and partial 28S large subunit (LSU) nrDNA and partial protein encoding genes including the RNA polymerase II second largest subunit (&lt;i&gt;RPB2&lt;/i&gt;), translation elongation factor 1-alpha (&lt;i&gt;TEF1&lt;/i&gt;) and β-tubulin (&lt;i&gt;TUB2&lt;/i&gt;). Based on these results, the subgenera &lt;i&gt;Astromata&lt;/i&gt;, &lt;i&gt;Bionectria&lt;/i&gt;, &lt;i&gt;Myronectria&lt;/i&gt; and &lt;i&gt;Zebrinella&lt;/i&gt; are supported within &lt;i&gt;Clonostachys&lt;/i&gt;. Furthermore, the genus &lt;i&gt;Sesquicillium&lt;/i&gt; is resurrected to accommodate the former subgenera &lt;i&gt;Epiphloea&lt;/i&gt; and &lt;i&gt;Uniparietina&lt;/i&gt;. The close relationship of &lt;i&gt;Clonostachys&lt;/i&gt; and &lt;i&gt;Sesquicillium&lt;/i&gt; is strongly supported as both are inferred phylogenetically as sister-genera. New taxa include 24 new species and 10 new combinations. Recognition of &lt;i&gt;Sesquicillium&lt;/i&gt; distinguishes species typically forming a reduced perithecial stroma superficially on plant tissue from species in &lt;i&gt;Clonostachys&lt;/i&gt; often forming well-developed, through bark erumpent stromata. The patterns of observed perithecial wall anatomies, perithecial wall and stroma interfaces, and asexual morph diversifications described in a previously compiled monograph are used for interpreting ancestral state reconstructions. It is inferred that the common ancestor of &lt;i&gt;Clonostachys&lt;/i&gt; and &lt;i&gt;Sesquicillium&lt;/i&gt; may have formed perithecia superficially on leaves, possessed a perithecial wall consisting of a single region, and formed intercalary phialides in penicilli of conidiophores. Character interpretation may also allow hypothesising that diversification of morphs occurred then in the two genera independent","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"1 1","pages":"205-266"},"PeriodicalIF":16.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11182609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69601202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Redisposition of acremonium-like fungi in <i>Hypocreales</i>.","authors":"L W Hou, A Giraldo, J Z Groenewald, T Rämä, R C Summerbell, G Z Huang, L Cai, P W Crous","doi":"10.3114/sim.2023.105.02","DOIUrl":"10.3114/sim.2023.105.02","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Acremonium&lt;/i&gt; is acknowledged as a highly ubiquitous genus including saprobic, parasitic, or endophytic fungi that inhabit a variety of environments. Species of this genus are extensively exploited in industrial, commercial, pharmaceutical, and biocontrol applications, and proved to be a rich source of novel and bioactive secondary metabolites. &lt;i&gt;Acremonium&lt;/i&gt; has been recognised as a taxonomically difficult group of ascomycetes, due to the reduced and high plasticity of morphological characters, wide ecological distribution and substrate range. Recent advances in molecular phylogenies, revealed that &lt;i&gt;Acremonium&lt;/i&gt; is highly polyphyletic and members of &lt;i&gt;Acremonium&lt;/i&gt; &lt;i&gt;s. lat.&lt;/i&gt; belong to at least three distinct orders of &lt;i&gt;Sordariomycetes&lt;/i&gt;, of which numerous orders, families and genera with acremonium-like morphs remain undefined. To infer the phylogenetic relationships and establish a natural classification for acremonium-like taxa, systematic analyses were conducted based on a large number of cultures with a global distribution and varied substrates. A total of 633 cultures with acremonium-like morphology, including 261 ex-type cultures from 89 countries and a variety of substrates including soil, plants, fungi, humans, insects, air, and water were examined. An overview phylogenetic tree based on three loci (ITS, LSU, &lt;i&gt;rpb2&lt;/i&gt;) was generated to delimit the orders and families. Separate trees based on a combined analysis of four loci (ITS, LSU, &lt;i&gt;rpb2&lt;/i&gt;, &lt;i&gt;tef-1α&lt;/i&gt;) were used to delimit species at generic and family levels. Combined with the morphological features, host associations and ecological analyses, acremonium-like species evaluated in the present study are currently assigned to 63 genera, and 14 families in &lt;i&gt;Cephalothecales,&lt;/i&gt; &lt;i&gt;Glomerellales&lt;/i&gt; and &lt;i&gt;Hypocreales&lt;/i&gt;, mainly in the families &lt;i&gt;Bionectriaceae&lt;/i&gt;, &lt;i&gt;Plectosphaerellaceae&lt;/i&gt; and &lt;i&gt;Sarocladiaceae&lt;/i&gt; and five new hypocrealean families, namely &lt;i&gt;Chrysonectriaceae&lt;/i&gt;, &lt;i&gt;Neoacremoniaceae&lt;/i&gt;, &lt;i&gt;Nothoacremoniaceae&lt;/i&gt;, &lt;i&gt;Pseudoniessliaceae&lt;/i&gt; and &lt;i&gt;Valsonectriaceae&lt;/i&gt;. Among them, 17 new genera and 63 new combinations are proposed, with descriptions of 65 new species. Furthermore, one epitype and one neotype are designated to stabilise the taxonomy and use of older names. Results of this study demonstrated that most species of &lt;i&gt;Acremonium&lt;/i&gt; &lt;i&gt;s. lat.&lt;/i&gt; grouped in genera of &lt;i&gt;Bionectriaceae&lt;/i&gt;, including the type &lt;i&gt;A&lt;/i&gt;. &lt;i&gt;alternatum&lt;/i&gt;. A phylogenetic backbone tree is provided for &lt;i&gt;Bionectriaceae&lt;/i&gt;, in which 183 species are recognised and 39 well-supported genera are resolved, including 10 new genera. Additionally, &lt;i&gt;rpb2&lt;/i&gt; and &lt;i&gt;tef-1α&lt;/i&gt; are proposed as potential DNA barcodes for the identification of taxa in &lt;i&gt;Bionectriaceae&lt;/i&gt;. &lt;b&gt;Taxonomic novelties: New families:&lt;/b&gt; &lt;i&gt;Chrysonectriaceae&lt;/i&gt; L.W. Hou, L. Cai & Crous, &lt;i&gt;Neoacremoniaceae&lt;/i&gt; L.W. Hou, L. Cai & Crous, &lt;i&gt;Nothoacremoniaceae&lt;/i&gt; L.W.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"1 1","pages":"23-203"},"PeriodicalIF":16.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11182610/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69601162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In search of lost ergots: phylogenetic re-evaluation of Claviceps species in Japan and their biogeographic patterns revealed","authors":"E. Tanaka, K. Tanada, T. Hosoe, B. Shrestha, M. Kolařík, M. Liu","doi":"10.3114/sim.2022.106.01","DOIUrl":"https://doi.org/10.3114/sim.2022.106.01","url":null,"abstract":"Claviceps (Clavicipitaceae, Hypocreales) was erected in 1853, although ergotism had been well-known for a much longer time. By 2000, about 70 taxa had been described in Claviceps, of which eight species and six varieties were based on Japanese type or authentic specimens. Most of these Japanese Claviceps taxa are based on lost specimens or have invalid names, which means many species practically exist only in the scientific literature. The ambiguous identities of these species have hindered taxonomic resolution of the genus Claviceps. Consequently, we sought and collected more than 300 fresh specimens in search of the lost Japanese ergots. Multilocus phylogenetic analyses based on DNA sequences from LSU, TEF-1α, TUB2, Mcm7, and RPB2 revealed the phylogenetic relationships between the Japanese specimens and known Claviceps spp., as well as the presence of biogeographic patterns. Based on the phylogenetic analysis, host range and morphology, we re-evaluated Japanese Claviceps and recognised at least 21 species in Japan. Here we characterised 14 previously described taxa and designated neo-, lecto- and epi-types for C. bothriochloae, C. imperatae, C. litoralis, C. microspora, C. panicoidearum and C. yanagawaensis. Two varieties were elevated to species rank with designated neotypes, i.e. C. agropyri and C. kawatanii. Six new species, C. miscanthicola, C. oplismeni, C. palustris, C. phragmitis, C. sasae and C. tandae were proposed and described.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"1 1","pages":""},"PeriodicalIF":16.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69600421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomy and systematics of the fungus-growing ant associate Escovopsis (Hypocreaceae)","authors":"Q.V. Montoya, M.J.S. Martiarena, A. Rodrigues","doi":"10.3114/sim.2023.106.06","DOIUrl":"https://doi.org/10.3114/sim.2023.106.06","url":null,"abstract":"Escovopsis is a symbiont of fungus-growing ant colonies. Unstandardised taxonomy prevented the evaluation of the morphological diversity of Escovopsis for more than a century. The aim of this study is to create a standardised taxonomic framework to assess the morphological and phylogenetic diversity of Escovopsis . Therefore, to set the foundation for Escovopsis taxonomy and allow interspecific comparisons within the genus, we redescribe the ex-type cultures of Escovopsis aspergilloides , E. clavata , E. lentecrescens , E. microspora , E. moelleri , E. multiformis , and E. weberi . Thus, based on the parameters adopted in this study combined with phylogenetic analyses using five molecular markers, we synonymize E. microspora with E. weberi , and introduce 13 new species isolated from attine nests collected in Argentina, Brazil, Costa Rica, Mexico, and Panama: E. breviramosa , E. chlamydosporosa , E. diminuta , E. elongatistipitata , E. gracilis , E. maculosa , E. papillata , E. peniculiformis , E. phialicopiosa , E. pseudocylindrica , E. rectangula , E. rosisimilis , and E. spicaticlavata . Our results revealed a great interspecific morphological diversity throughout Escovopsis . Notwithstanding, colony growth rates at different temperatures, as well as vesicle shape, appear to be the most outstanding features distinguishing species in the genus. This study fills an important gap in the systematics of Escovopsis that will allow future researchers to unravel the genetic and morphological diversity and species diversification of these attine ant symbionts.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135758459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phytophthora: taxonomic and phylogenetic revision of the genus","authors":"Z.G. Abad, T.I. Burgess, T. Bourret, K. Bensch, S.O. Cacciola, B. Scanu, R. Mathew, B. Kasiborski, S. Srivastava, K. Kageyama, J.C. Bienapfl, G. Verkleij, K. Broders, L. Schena, A.J. Redford","doi":"10.3114/sim.2023.106.05","DOIUrl":"https://doi.org/10.3114/sim.2023.106.05","url":null,"abstract":"Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani , P. honggalleglyana (Synonym: P. hydropathica ), P. megakarya , P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, β-tub , COI , EF1α , HSP90 , L10 , and YPT1 ) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the “ IDphy : molecular and morphological identification of Phytophthora based on the types” online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI ) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora , widely considered one of the most important genera of plant pathogens.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136008335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The subfamily Xerocomoideae (Boletaceae, Boletales) in China","authors":"R. Xue, X. Zhang, C. Xu, H. Xie, L.L. Wu, Y. Wang, L. Tang, Y. Hao, K. Zhao, S. Jiang, Y. Li, Y.Y. Yang, Z. Li, Z. Liang, N. Zeng","doi":"10.3114/sim.2022.106.03","DOIUrl":"https://doi.org/10.3114/sim.2022.106.03","url":null,"abstract":"Xerocomoideae is an ecologically and economically important Boletaceae subfamily (Boletales) comprising 10 genera. Although many studies have focused on Xerocomoideae in China, the diversity, taxonomy and molecular phylogeny still remained incompletely understood. In the present study, taxonomic and phylogenetic studies on Chinese species of Xerocomoideae were carried out by morphological examinations and molecular phylogenetic analyses. Eight genera in Xerocomoideae, viz. Aureoboletus, Boletellus, Heimioporus, Hemileccinum, Hourangia, Phylloporus, Pulchroboletus, and Xerocomus were confirmed to be distributed in China; 97 species of the subfamily were accepted as being distributed in China; one ambiguous taxon was tentatively named Bol. aff. putuoensis; two synonyms, viz. A. marroninus and P. dimorphus were defined. Among the Chinese accepted species, 13 were newly described, viz. A. albipes, A. conicus, A. ornatipes, Bol. erythrolepis, Bol. rubidus, Bol. sinochrysenteroides, Bol. subglobosus, Bol. zenghuoxingii, H. squamipes, P. hainanensis, Pul. erubescens, X. albotomentosus, and X. fuscatus, 36 known species were redescribed, and the other 48 species were reviewed. Keys to accepted species of Aureoboletus, Boletellus, Heimioporus, Hemileccinum, Hourangia, Phylloporus, and Xerocomus in China were also provided.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"1 1","pages":""},"PeriodicalIF":16.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69600489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina-Supplementary files","authors":"M. Groenewald","doi":"10.3114/sim.2023.105.01_supp","DOIUrl":"https://doi.org/10.3114/sim.2023.105.01_supp","url":null,"abstract":"Lv:0:53:http://www.w3.org/1999/02/22-rdf-syntax-ns#XMLLiteral<xhtml:span xmlns:xhtml=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\">Supplementary files to this article: Fig S1, Tables S1-S3.</xhtml:span>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"28 1-2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136092822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomy of <i>Aspergillus</i> series <i>Versicolores</i>: species reduction and lessons learned about intraspecific variability.","authors":"F Sklenář, K Glässnerová, Ž Jurjević, J Houbraken, R A Samson, C M Visagie, N Yilmaz, J Gené, J Cano, A J Chen, A Nováková, T Yaguchi, M Kolařík, V Hubka","doi":"10.3114/sim.2022.102.02","DOIUrl":"10.3114/sim.2022.102.02","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Aspergillus&lt;/i&gt; series &lt;i&gt;Versicolores&lt;/i&gt; members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (&lt;i&gt;CaM&lt;/i&gt;) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (&lt;i&gt;benA&lt;/i&gt;, &lt;i&gt;CaM&lt;/i&gt;, &lt;i&gt;RPB2&lt;/i&gt;, &lt;i&gt;Mcm7&lt;/i&gt;, &lt;i&gt;Tsr1&lt;/i&gt;). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series &lt;i&gt;Versicolores&lt;/i&gt; to four species, namely &lt;i&gt;A.&lt;/i&gt; &lt;i&gt;versicolor, A. creber&lt;/i&gt;, &lt;i&gt;A. sydowii&lt;/i&gt; and &lt;i&gt;A. subversicolor&lt;/i&gt;, and the remaining species are synonymized with either &lt;i&gt;A. versicolor&lt;/i&gt; or &lt;i&gt;A. creber&lt;/i&gt;. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between &lt;i&gt;A. versicolor&lt;/i&gt; and &lt;i&gt;A. creber&lt;/i&gt;. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied &lt;i&gt;Aspergillus&lt;/i&gt; species complexes and other fungal genera. &lt;b&gt;Citation:&lt;/b&gt; Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilm","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"102 ","pages":"53-93"},"PeriodicalIF":14.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9240641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}