Studies in Mycology最新文献

{"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}

{"title":"A monograph of <i>Aspergillus</i> section <i>Candidi</i>.","authors":"K Glässnerová,&nbsp;F Sklenář,&nbsp;Ž Jurjević,&nbsp;J Houbraken,&nbsp;T Yaguchi,&nbsp;C M Visagie,&nbsp;J Gené,&nbsp;J P Z Siqueira,&nbsp;A Kubátová,&nbsp;M Kolařík,&nbsp;V Hubka","doi":"10.3114/sim.2022.102.01","DOIUrl":"https://doi.org/10.3114/sim.2022.102.01","url":null,"abstract":"<p><p><i>Aspergillus</i> section <i>Candidi</i> encompasses white- or yellow-sporulating species mostly isolated from indoor and cave environments, food, feed, clinical material, soil and dung. Their identification is non-trivial due to largely uniform morphology. This study aims to re-evaluate the species boundaries in the section <i>Candidi</i> and present an overview of all existing species along with information on their ecology. For the analyses, we assembled a set of 113 strains with diverse origin. For the molecular analyses, we used DNA sequences of three house-keeping genes (<i>benA</i>, <i>CaM</i> and <i>RPB2</i>) and employed species delimitation methods based on a multispecies coalescent model. Classical phylogenetic methods and genealogical concordance phylogenetic species recognition (GCPSR) approaches were used for comparison. Phenotypic studies involved comparisons of macromorphology on four cultivation media, seven micromorphological characters and growth at temperatures ranging from 10 to 45 °C. Based on the integrative approach comprising four criteria (phylogenetic and phenotypic), all currently accepted species gained support, while two new species are proposed (<i>A. magnus</i> and <i>A. tenebricus</i>). In addition, we proposed the new name <i>A. neotritici</i> to replace an invalidly described <i>A. tritici</i>. The revised section <i>Candidi</i> now encompasses nine species, some of which manifest a high level of intraspecific genetic and/or phenotypic variability (<i>e.g.</i>, <i>A. subalbidus</i> and <i>A. campestris</i>) while others are more uniform (<i>e.g.</i>, <i>A. candidus</i> or <i>A. pragensis</i>). The growth rates on different media and at different temperatures, colony colours, production of soluble pigments, stipe dimensions and vesicle diameters contributed the most to the phenotypic species differentiation. <b>Taxonomic novelties: New species:</b> <i>Aspergillus magnus</i> Glässnerová & Hubka; <i>Aspergillus neotritici</i> Glässnerová & Hubka; <i>Aspergillus tenebricus</i> Houbraken, Glässnerová & Hubka. <b>Citation:</b> Glässnerová K, Sklenář F, Jurjević Ž, Houbraken J, Yaguchi T, Visagie CM, Gené J, Siqueira JPZ, Kubátová A, Kolařík M, Hubka V (2022). A monograph of <i>Aspergillus</i> section <i>Candidi</i>. <i>Studies in Mycology</i> <b>102</b>: 1-51. doi: 10.3114/sim.2022.102.01.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"102 ","pages":"1-51"},"PeriodicalIF":16.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10330037","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":"Reducing the number of accepted species in <i>Aspergillus</i> series <i>Nigri</i>.","authors":"C Bian, Y Kusuya, F Sklenář, E D'hooge, T Yaguchi, S Ban, C M Visagie, J Houbraken, H Takahashi, V Hubka","doi":"10.3114/sim.2022.102.03","DOIUrl":"10.3114/sim.2022.102.03","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The &lt;i&gt;Aspergillus&lt;/i&gt; series &lt;i&gt;Nigri&lt;/i&gt; contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (&lt;i&gt;benA&lt;/i&gt;, &lt;i&gt;CaM&lt;/i&gt; and &lt;i&gt;RPB2&lt;/i&gt;) for 276 strains from series &lt;i&gt;Nigri&lt;/i&gt; and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: &lt;i&gt;A. niger&lt;/i&gt;, &lt;i&gt;A. tubingensis&lt;/i&gt; and &lt;i&gt;A. brasiliensis&lt;/i&gt;. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on &lt;i&gt;benA&lt;/i&gt;, &lt;i&gt;CaM&lt;/i&gt; and &lt;i&gt;RPB2&lt;/i&gt; is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the &lt;i&gt;A. niger&lt;/i&gt; and &lt;i&gt;A. brasiliensis&lt;/i&gt; lineages, while one to four species were inconsistently delimited in the &lt;i&gt;A. tubingensis&lt;/i&gt; lineage. After considering all of these results and their practical implications, we propose that the revised series &lt;i&gt;Nigri&lt;/i&gt; includes six species: &lt;i&gt;A. brasiliensis&lt;/i&gt;, &lt;i&gt;A. eucalypticola&lt;/i&gt;, &lt;i&gt;A. luchuensis&lt;/i&gt; (syn&lt;i&gt;. A. piperis&lt;/i&gt;), &lt;i&gt;A. niger&lt;/i&gt; (syn. &lt;i&gt;A. vinaceus&lt;/i&gt; and &lt;i&gt;A. welwitschiae&lt;/i&gt;), &lt;i&gt;A. tubingensis&lt;/i&gt; (syn. &lt;i&gt;A. chiangmaiensis&lt;/i&gt;, &lt;i&gt;A. costaricensis&lt;/i&gt;, &lt;i&gt;A. neoniger&lt;/i&gt; and &lt;i&gt;A. pseudopiperis&lt;/i&gt;) and &lt;i&gt;A. vadensis&lt;/i&gt;. We also showed that the intraspecific genetic variability in the redefined &lt;i&gt;A. niger&lt;/i&gt; and &lt;i&gt;A. tubingensis&lt;/i&gt; does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy. &lt;b&gt;Cita","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"102 ","pages":"95-132"},"PeriodicalIF":14.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9240643","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}