Studies in Mycology最新文献

{"title":"Updating the taxonomy of Aspergillus in South Africa","authors":"C.M. Visagie ,&nbsp;J. Houbraken","doi":"10.1016/j.simyco.2020.02.003","DOIUrl":"10.1016/j.simyco.2020.02.003","url":null,"abstract":"<div><p>The taxonomy and nomenclature of the genus <em>Aspergillus</em> and its associated sexual (teleomorphic) genera have been greatly stabilised over the last decade. This was in large thanks to the accepted species list published in 2014 and associated metadata such as DNA reference sequences released at the time. It had a great impact on the community and it has never been easier to identify, publish and describe the missing <em>Aspergillus</em> diversity. To further stabilise its taxonomy, it is crucial to not only discover and publish new species but also to capture infraspecies variation in the form of DNA sequences. This data will help to better characterise and distinguish existing species and make future identifications more robust. South Africa has diverse fungal communities but remains largely unexplored in terms of <em>Aspergillus</em> with very few sequences available for local strains. In this paper, we re-identify <em>Aspergillus</em> previously accessioned in the PPRI and MRC culture collections using modern taxonomic approaches. In the process, we re-identify strains to 63 species, describe seven new species and release a large number of new DNA reference sequences.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"95 ","pages":"Pages 253-292"},"PeriodicalIF":16.5,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2020.02.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38318131","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":"Foliar pathogens of eucalypts","authors":"P.W. Crous ,&nbsp;M.J. Wingfield ,&nbsp;R. Cheewangkoon ,&nbsp;A.J. Carnegie ,&nbsp;T.I. Burgess ,&nbsp;B.A. Summerell ,&nbsp;J. Edwards ,&nbsp;P.W.J. Taylor ,&nbsp;J.Z. Groenewald","doi":"10.1016/j.simyco.2019.08.001","DOIUrl":"10.1016/j.simyco.2019.08.001","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Species of eucalypts are commonly cultivated for solid wood and pulp products. The expansion of commercially managed eucalypt plantations has chiefly been driven by their rapid growth and suitability for propagation across a very wide variety of sites and climatic conditions. Infection of foliar fungal pathogens of eucalypts is resulting in increasingly negative impacts on commercial forest industries globally. To assist in evaluating this threat, the present study provides a global perspective on foliar pathogens of eucalypts. We treat 110 different genera including species associated with foliar disease symptoms of these hosts. The vast majority of these fungi have been grown in axenic culture, and subjected to DNA sequence analysis, resolving their phylogeny. During the course of this study several new genera and species were encountered, and these are described. New genera include: &lt;em&gt;Lembosiniella&lt;/em&gt; (&lt;em&gt;L. eucalyptorum&lt;/em&gt; on &lt;em&gt;E. dunnii,&lt;/em&gt; Australia), &lt;em&gt;Neosonderhenia&lt;/em&gt; (&lt;em&gt;N. eucalypti&lt;/em&gt; on &lt;em&gt;E. costata,&lt;/em&gt; Australia), &lt;em&gt;Neothyriopsis&lt;/em&gt; (&lt;em&gt;N. sphaerospora&lt;/em&gt; on &lt;em&gt;E. camaldulensis&lt;/em&gt;, South Africa), &lt;em&gt;Neotrichosphaeria&lt;/em&gt; (&lt;em&gt;N. eucalypticola&lt;/em&gt; on &lt;em&gt;E. deglupta&lt;/em&gt;, Australia), &lt;em&gt;Nothotrimmatostroma&lt;/em&gt; (&lt;em&gt;N. bifarium&lt;/em&gt; on &lt;em&gt;E. dalrympleana&lt;/em&gt;, Australia), &lt;em&gt;Nowamyces&lt;/em&gt; (incl. &lt;em&gt;Nowamycetaceae fam. nov&lt;/em&gt;., &lt;em&gt;N. globulus&lt;/em&gt; on &lt;em&gt;E. globulus&lt;/em&gt;, Australia), and &lt;em&gt;Walkaminomyces&lt;/em&gt; (&lt;em&gt;W. medusae&lt;/em&gt; on &lt;em&gt;E. alba&lt;/em&gt;, Australia). New species include (all from Australia): &lt;em&gt;Disculoides fraxinoides&lt;/em&gt; on &lt;em&gt;E. fraxinoides, Elsinoe piperitae on E. piperita, Fusculina regnans&lt;/em&gt; on &lt;em&gt;E. regnans, Marthamyces johnstonii&lt;/em&gt; on &lt;em&gt;E. dunnii&lt;/em&gt;, &lt;em&gt;Neofusicoccum corticosae&lt;/em&gt; on &lt;em&gt;E. corticosa&lt;/em&gt;, &lt;em&gt;Neotrimmatostroma dalrympleanae&lt;/em&gt; on &lt;em&gt;E. dalrympleana, Nowamyces piperitae&lt;/em&gt; on &lt;em&gt;E. piperita&lt;/em&gt;, &lt;em&gt;Phaeothyriolum dunnii&lt;/em&gt; on &lt;em&gt;E. dunnii&lt;/em&gt;, &lt;em&gt;Pseudophloeospora eucalyptigena&lt;/em&gt; on &lt;em&gt;E. obliqua&lt;/em&gt;, &lt;em&gt;Pseudophloeospora jollyi&lt;/em&gt; on &lt;em&gt;Eucalyptus&lt;/em&gt; sp., &lt;em&gt;Quambalaria tasmaniae&lt;/em&gt; on &lt;em&gt;Eucalyptus&lt;/em&gt; sp., &lt;em&gt;Q. rugosae&lt;/em&gt; on &lt;em&gt;E. rugosa&lt;/em&gt;, &lt;em&gt;Sonderhenia radiata&lt;/em&gt; on &lt;em&gt;E. radiata&lt;/em&gt;, &lt;em&gt;Teratosphaeria pseudonubilosa&lt;/em&gt; on &lt;em&gt;E. globulus&lt;/em&gt; and &lt;em&gt;Thyrinula dunnii&lt;/em&gt; on &lt;em&gt;E. dunnii&lt;/em&gt;. A new name is also proposed for &lt;em&gt;Heteroconium eucalypti&lt;/em&gt; as &lt;em&gt;Thyrinula uruguayensis&lt;/em&gt; on &lt;em&gt;E. dunnii&lt;/em&gt;, Uruguay. Although many of these genera and species are commonly associated with disease problems, several appear to be opportunists developing on stressed or dying tissues. For the majority of these fungi, pathogenicity remains to be determined. This represents an important goal for forest pathologists and biologists in the future. Consequently, this study will promote renewed interest in foliar pathogens of eucalypts, leading to investigations that will provide an impr","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"94 ","pages":"Pages 125-298"},"PeriodicalIF":16.5,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2019.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41213510","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":"Genera of phytopathogenic fungi: GOPHY 3","authors":"Y. Marin-Felix ,&nbsp;M. Hernández-Restrepo ,&nbsp;I. Iturrieta-González ,&nbsp;D. García ,&nbsp;J. Gené ,&nbsp;J.Z. Groenewald ,&nbsp;L. Cai ,&nbsp;Q. Chen ,&nbsp;W. Quaedvlieg ,&nbsp;R.K. Schumacher ,&nbsp;P.W.J. Taylor ,&nbsp;C. Ambers ,&nbsp;G. Bonthond ,&nbsp;J. Edwards ,&nbsp;S.A. Krueger-Hadfield ,&nbsp;J.J. Luangsa-ard ,&nbsp;L. Morton ,&nbsp;A. Moslemi ,&nbsp;M. Sandoval-Denis ,&nbsp;Y.P. Tan ,&nbsp;P.W. Crous","doi":"10.1016/j.simyco.2019.05.001","DOIUrl":"10.1016/j.simyco.2019.05.001","url":null,"abstract":"<div><p>This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: <em>Allophoma</em>, <em>Alternaria</em>, <em>Brunneosphaerella</em>, <em>Elsinoe</em>, <em>Exserohilum</em>, <em>Neosetophoma</em>, <em>Neostagonospora</em>, <em>Nothophoma</em>, <em>Parastagonospora</em>, <em>Phaeosphaeriopsis</em>, <em>Pleiocarpon</em>, <em>Pyrenophora</em>, <em>Ramichloridium</em>, <em>Seifertia</em>, <em>Seiridium</em>, <em>Septoriella</em>, <em>Setophoma</em>, <em>Stagonosporopsis</em>, <em>Stemphylium</em>, <em>Tubakia</em> and <em>Zasmidium</em>. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"94 ","pages":"Pages 1-124"},"PeriodicalIF":16.5,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2019.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41213511","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":"Taxonomy of Aspergillus section Flavi and their production of aflatoxins, ochratoxins and other mycotoxins","authors":"J.C. Frisvad ,&nbsp;V. Hubka ,&nbsp;C.N. Ezekiel ,&nbsp;S.-B. Hong ,&nbsp;A. Nováková ,&nbsp;A.J. Chen ,&nbsp;M. Arzanlou ,&nbsp;T.O. Larsen ,&nbsp;F. Sklenář ,&nbsp;W. Mahakarnchanakul ,&nbsp;R.A. Samson ,&nbsp;J. Houbraken","doi":"10.1016/j.simyco.2018.06.001","DOIUrl":"10.1016/j.simyco.2018.06.001","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Aflatoxins and ochratoxins are among the most important mycotoxins of all and producers of both types of mycotoxins are present in &lt;em&gt;Aspergillus&lt;/em&gt; section &lt;em&gt;Flavi&lt;/em&gt;, albeit never in the same species. Some of the most efficient producers of aflatoxins and ochratoxins have not been described yet. Using a polyphasic approach combining phenotype, physiology, sequence and extrolite data, we describe here eight new species in section &lt;em&gt;Flavi&lt;/em&gt;. Phylogenetically, section &lt;em&gt;Flavi&lt;/em&gt; is split in eight clades and the section currently contains 33 species. Two species only produce aflatoxin B&lt;sub&gt;1&lt;/sub&gt; and B&lt;sub&gt;2&lt;/sub&gt; (&lt;em&gt;A. pseudotamarii&lt;/em&gt; and &lt;em&gt;A. togoensis&lt;/em&gt;), and 14 species are able to produce aflatoxin B&lt;sub&gt;1&lt;/sub&gt;, B&lt;sub&gt;2&lt;/sub&gt;, G&lt;sub&gt;1&lt;/sub&gt; and G&lt;sub&gt;2&lt;/sub&gt;: three newly described species &lt;em&gt;A. aflatoxiformans, A. austwickii&lt;/em&gt; and &lt;em&gt;A. cerealis&lt;/em&gt; in addition to &lt;em&gt;A. arachidicola&lt;/em&gt;, &lt;em&gt;A. minisclerotigenes&lt;/em&gt;, &lt;em&gt;A. mottae, A. luteovirescens&lt;/em&gt; (formerly &lt;em&gt;A. bombycis&lt;/em&gt;)&lt;em&gt;, A. nomius, A. novoparasiticus, A. parasiticus, A. pseudocaelatus, A. pseudonomius, A. sergii&lt;/em&gt; and &lt;em&gt;A. transmontanensis&lt;/em&gt;. It is generally accepted that &lt;em&gt;A. flavus&lt;/em&gt; is unable to produce type G aflatoxins, but here we report on Korean strains that also produce aflatoxin G&lt;sub&gt;1&lt;/sub&gt; and G&lt;sub&gt;2&lt;/sub&gt;. One strain of &lt;em&gt;A. bertholletius&lt;/em&gt; can produce the immediate aflatoxin precursor 3-O-methylsterigmatocystin, and one strain of &lt;em&gt;Aspergillus sojae&lt;/em&gt; and two strains of &lt;em&gt;Aspergillus alliaceus&lt;/em&gt; produced versicolorins. Strains of the domesticated forms of &lt;em&gt;A. flavus&lt;/em&gt; and &lt;em&gt;A. parasiticus&lt;/em&gt;, &lt;em&gt;A. oryzae&lt;/em&gt; and &lt;em&gt;A. sojae&lt;/em&gt;, respectively, lost their ability to produce aflatoxins, and from the remaining phylogenetically closely related species (belonging to the &lt;em&gt;A. flavus&lt;/em&gt;-, &lt;em&gt;A. tamarii&lt;/em&gt;-, &lt;em&gt;A. bertholletius&lt;/em&gt;- and &lt;em&gt;A. nomius&lt;/em&gt;-clades), only &lt;em&gt;A. caelatus&lt;/em&gt;, &lt;em&gt;A. subflavus&lt;/em&gt; and &lt;em&gt;A. tamarii&lt;/em&gt; are unable to produce aflatoxins. With exception of &lt;em&gt;A. togoensis&lt;/em&gt; in the &lt;em&gt;A. coremiiformis&lt;/em&gt;-clade, all species in the phylogenetically more distant clades (&lt;em&gt;A. alliaceus&lt;/em&gt;-, &lt;em&gt;A. coremiiformis&lt;/em&gt;-, &lt;em&gt;A. leporis&lt;/em&gt;- and &lt;em&gt;A. avenaceus&lt;/em&gt;-clade) are unable to produce aflatoxins. Three out of the four species in the &lt;em&gt;A. alliaceus&lt;/em&gt;-clade can produce the mycotoxin ochratoxin A: &lt;em&gt;A. alliaceus s&lt;/em&gt;. &lt;em&gt;str&lt;/em&gt;. and two new species described here as &lt;em&gt;A. neoalliaceus&lt;/em&gt; and &lt;em&gt;A. vandermerwei&lt;/em&gt;. Eight species produced the mycotoxin tenuazonic acid: &lt;em&gt;A. bertholletius&lt;/em&gt;, &lt;em&gt;A. caelatus, A. luteovirescens&lt;/em&gt;, &lt;em&gt;A. nomius, A. pseudocaelatus&lt;/em&gt;, &lt;em&gt;A. pseudonomius, A. pseudotamarii&lt;/em&gt; and &lt;em&gt;A. tamarii&lt;/em&gt; while the related mycotoxin cyclopiazonic acid was produced by 13 species: &lt;em&gt;A. aflatoxiformans, A. austwickii, A. bertholletius, A. cerealis, A. flavus, A. minisclerotigenes, ","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"93 ","pages":"Pages 1-63"},"PeriodicalIF":16.5,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.06.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36398323","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":"Redefining Humicola sensu stricto and related genera in the Chaetomiaceae","authors":"X.W. Wang ,&nbsp;F.Y. Yang ,&nbsp;M. Meijer ,&nbsp;B. Kraak ,&nbsp;B.D. Sun ,&nbsp;Y.L. Jiang ,&nbsp;Y.M. Wu ,&nbsp;F.Y. Bai ,&nbsp;K.A. Seifert ,&nbsp;P.W. Crous ,&nbsp;R.A. Samson ,&nbsp;J. Houbraken","doi":"10.1016/j.simyco.2018.07.001","DOIUrl":"10.1016/j.simyco.2018.07.001","url":null,"abstract":"&lt;div&gt;&lt;p&gt;The traditional concept of the genus &lt;em&gt;Humicola&lt;/em&gt; includes species that produce pigmented, thick-walled and single-celled spores laterally or terminally on hyphae or minimally differentiated conidiophores. More than 50 species have been described in the genus. Species commonly occur in soil, indoor environments, and compost habitats. The taxonomy of &lt;em&gt;Humicola&lt;/em&gt; and morphologically similar genera is poorly understood in modern terms. Based on a four-locus phylogeny, the morphological concept of &lt;em&gt;Humicola&lt;/em&gt; proved to be polyphyletic. The type of &lt;em&gt;Humicola&lt;/em&gt;, &lt;em&gt;H. fuscoatra&lt;/em&gt;, belongs to the &lt;em&gt;Chaetomiaceae&lt;/em&gt;. In the &lt;em&gt;Chaetomiaceae&lt;/em&gt;, species producing humicola-like thick-walled spores are distributed among four lineages: &lt;em&gt;Humicola sensu stricto&lt;/em&gt;, &lt;em&gt;Mycothermus&lt;/em&gt;, &lt;em&gt;Staphylotrichum,&lt;/em&gt; and &lt;em&gt;Trichocladium&lt;/em&gt;. In our revised concept of &lt;em&gt;Humicola&lt;/em&gt;, asexual and sexually reproducing species both occur. The re-defined &lt;em&gt;Humicola&lt;/em&gt; contains 24 species (seven new and thirteen new combinations), which are described and illustrated in this study. The species in this genus produce conidia that are lateral, intercalary or terminal on/in hyphae, and conidiophores are not formed or are minimally developed (micronematous). The ascospores of sexual &lt;em&gt;Humicola&lt;/em&gt; species are limoniform to quadrangular in face view and bilaterally flattened with one apical germ pore. Seven species are accepted in &lt;em&gt;Staphylotrichum&lt;/em&gt; (four new species, one new combination). Thick-walled conidia of &lt;em&gt;Staphylotrichum&lt;/em&gt; species usually arise either from hyphae (micronematous) or from apically branched, seta-like conidiophores (macronematous). The sexual morph represented by &lt;em&gt;Staphylotrichum longicolleum&lt;/em&gt; (= &lt;em&gt;Chaetomium longicolleum&lt;/em&gt;) produces ascomata with long necks composed of a fused basal part of the terminal hairs, and ascospores that are broad limoniform to nearly globose, bilaterally flattened, with an apical germ pore. The &lt;em&gt;Trichocladium&lt;/em&gt; lineage has a high morphological diversity in both asexual and sexual structures. Phylogenetic analysis revealed four subclades in this lineage. However, these subclades are genetically closely related, and no distinctive phenotypic characters are linked to any of them. Fourteen species are accepted in &lt;em&gt;Trichocladium,&lt;/em&gt; including one new species, twelve new combinations. The type species of &lt;em&gt;Gilmaniella&lt;/em&gt;, &lt;em&gt;G. humicola&lt;/em&gt;, belongs to the polyphyletic family &lt;em&gt;Lasiosphaeriaceae&lt;/em&gt; (&lt;em&gt;Sordariales&lt;/em&gt;), but &lt;em&gt;G. macrospora&lt;/em&gt; phylogenetically belongs to &lt;em&gt;Trichocladium&lt;/em&gt;. The thermophilic genus &lt;em&gt;Mycothermus&lt;/em&gt; and the type species &lt;em&gt;My. thermophilum&lt;/em&gt; are validated, and one new &lt;em&gt;Mycothermus&lt;/em&gt; species is described. Phylogenetic analyses show that &lt;em&gt;Remersonia&lt;/em&gt;, another thermophilic genus, is sister to &lt;em&gt;Mycothermus&lt;/em&gt; and two species are known, including one new species. &lt;em&gt;The","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"93 ","pages":"Pages 65-153"},"PeriodicalIF":16.5,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.07.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36487722","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":"Phylogenetic re-evaluation of Thielavia with the introduction of a new family Podosporaceae","authors":"X.W. Wang ,&nbsp;F.Y. Bai ,&nbsp;K. Bensch ,&nbsp;M. Meijer ,&nbsp;B.D. Sun ,&nbsp;Y.F. Han ,&nbsp;P.W. Crous ,&nbsp;R.A. Samson ,&nbsp;F.Y. Yang ,&nbsp;J. Houbraken","doi":"10.1016/j.simyco.2019.08.002","DOIUrl":"10.1016/j.simyco.2019.08.002","url":null,"abstract":"&lt;div&gt;&lt;p&gt;The genus &lt;em&gt;Thielavia&lt;/em&gt; is morphologically defined by having non-ostiolate ascomata with a thin peridium composed of &lt;em&gt;textura epidermoidea&lt;/em&gt;, and smooth, single-celled, pigmented ascospores with one germ pore. &lt;em&gt;Thielavia&lt;/em&gt; is typified with &lt;em&gt;Th. basicola&lt;/em&gt; that grows in close association with a hyphomycete which was traditionally identified as &lt;em&gt;Thielaviopsis basicola&lt;/em&gt;. Besides &lt;em&gt;Th. basicola&lt;/em&gt; exhibiting the mycoparasitic nature, the majority of the described &lt;em&gt;Thielavia&lt;/em&gt; species are from soil, and some have economic and ecological importance. Unfortunately, no living type material of &lt;em&gt;Th. basicola&lt;/em&gt; exists, hindering a proper understanding of the classification of &lt;em&gt;Thielavia&lt;/em&gt;. Therefore, &lt;em&gt;Thielavia basicola&lt;/em&gt; was neotypified by material of a mycoparasite presenting the same ecology and morphology as described in the original description. We subsequently performed a multi-gene phylogenetic analyses (&lt;em&gt;rpb2&lt;/em&gt;, &lt;em&gt;tub2&lt;/em&gt;, ITS and LSU) to resolve the phylogenetic relationships of the species currently recognised in &lt;em&gt;Thielavia&lt;/em&gt;. Our results demonstrate that &lt;em&gt;Thielavia&lt;/em&gt; is highly polyphyletic, being related to three family-level lineages in two orders. The redefined genus &lt;em&gt;Thielavia&lt;/em&gt; is restricted to its type species, &lt;em&gt;Th. basicola&lt;/em&gt;, which belongs to the &lt;em&gt;Ceratostomataceae&lt;/em&gt; (&lt;em&gt;Melanosporales&lt;/em&gt;) and its host is demonstrated to be &lt;em&gt;Berkeleyomyces rouxiae&lt;/em&gt;, one of the two species in the “&lt;em&gt;Thielaviopsis basicola&lt;/em&gt;” species complex. The new family &lt;em&gt;Podosporaceae&lt;/em&gt; is sister to the &lt;em&gt;Chaetomiaceae&lt;/em&gt; in the &lt;em&gt;Sordariales&lt;/em&gt; and accommodates the re-defined genera &lt;em&gt;Podospora&lt;/em&gt;, &lt;em&gt;Trangularia&lt;/em&gt; and &lt;em&gt;Cladorrhinum&lt;/em&gt;, with the last genus including two former &lt;em&gt;Thielavia&lt;/em&gt; species (&lt;em&gt;Th. hyalocarpa&lt;/em&gt; and &lt;em&gt;Th. intermedia&lt;/em&gt;). This family also includes the genetic model species &lt;em&gt;Podospora anserina&lt;/em&gt;, which was combined in &lt;em&gt;Triangularia&lt;/em&gt; (as &lt;em&gt;Triangularia anserina&lt;/em&gt;). The remaining &lt;em&gt;Thielavia&lt;/em&gt; species fall in ten unrelated clades in the &lt;em&gt;Chaetomiaceae&lt;/em&gt;, leading to the proposal of nine new genera (&lt;em&gt;Carteria&lt;/em&gt;, &lt;em&gt;Chrysanthotrichum&lt;/em&gt;, &lt;em&gt;Condenascus&lt;/em&gt;, &lt;em&gt;Hyalosphaerella&lt;/em&gt;, &lt;em&gt;Microthielavia&lt;/em&gt;, &lt;em&gt;Parathielavia&lt;/em&gt;, &lt;em&gt;Pseudothielavia&lt;/em&gt;, &lt;em&gt;Stolonocarpus&lt;/em&gt; and &lt;em&gt;Thermothielavioides&lt;/em&gt;). The genus &lt;em&gt;Canariomyces&lt;/em&gt; is transferred from &lt;em&gt;Microascaceae&lt;/em&gt; (&lt;em&gt;Microascales&lt;/em&gt;) to &lt;em&gt;Chaetomiaceae&lt;/em&gt; based on its type species &lt;em&gt;Can. notabilis&lt;/em&gt;. &lt;em&gt;Canariomyces&lt;/em&gt; is closely related to the human-pathogenic genus &lt;em&gt;Madurella&lt;/em&gt;, and includes three thielavia-like species and one novel species. Three monotypic genera with a chaetomium-like morph (&lt;em&gt;Brachychaeta, Chrysocorona&lt;/em&gt; and &lt;em&gt;Floropilus&lt;/em&gt;) are introduced to better resolve the &lt;em&gt;Chaetomiaceae&lt;/em&gt; and the thielavia-like species in the family. &lt;","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"93 ","pages":"Pages 155-252"},"PeriodicalIF":16.5,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2019.08.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37447110","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":"Genera of phytopathogenic fungi: GOPHY 2","authors":"Y. Marin-Felix ,&nbsp;M. Hernández-Restrepo ,&nbsp;M.J. Wingfield ,&nbsp;A. Akulov ,&nbsp;A.J. Carnegie ,&nbsp;R. Cheewangkoon ,&nbsp;D. Gramaje ,&nbsp;J.Z. Groenewald ,&nbsp;V. Guarnaccia ,&nbsp;F. Halleen ,&nbsp;L. Lombard ,&nbsp;J. Luangsa-ard ,&nbsp;S. Marincowitz ,&nbsp;A. Moslemi ,&nbsp;L. Mostert ,&nbsp;W. Quaedvlieg ,&nbsp;R.K. Schumacher ,&nbsp;C.F.J. Spies ,&nbsp;R. Thangavel ,&nbsp;P.W.J. Taylor ,&nbsp;P.W. Crous","doi":"10.1016/j.simyco.2018.04.002","DOIUrl":"10.1016/j.simyco.2018.04.002","url":null,"abstract":"<div><p>This paper represents the second contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information regarding the pathology, distribution, hosts and disease symptoms for the treated genera. In addition, primary and secondary DNA barcodes for the currently accepted species are included. This second paper in the GOPHY series treats 20 genera of phytopathogenic fungi and their relatives including: <em>Allantophomopsiella, Apoharknessia, Cylindrocladiella, Diaporthe, Dichotomophthora, Gaeumannomyces, Harknessia, Huntiella, Macgarvieomyces, Metulocladosporiella, Microdochium, Oculimacula, Paraphoma, Phaeoacremonium, Phyllosticta, Proxypiricularia, Pyricularia, Stenocarpella</em>, <em>Utrechtiana</em> and <em>Wojnowiciella</em>. This study includes the new genus <em>Pyriculariomyces</em>, 20 new species, five new combinations, and six typifications for older names.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"92 ","pages":"Pages 47-133"},"PeriodicalIF":16.5,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.04.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36305025","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":"Inside Plectosphaerellaceae","authors":"A. Giraldo ,&nbsp;P.W. Crous","doi":"10.1016/j.simyco.2018.10.005","DOIUrl":"10.1016/j.simyco.2018.10.005","url":null,"abstract":"<div><p>The family <em>Plectosphaerellaceae</em> (<em>Glomerellales</em>, <em>Sordariomycetes</em>) includes numerous plant pathogenic genera and soil-borne fungal species. Ten genera are currently accepted, including several taxa that occupy an unresolved position within the family. To address this issue, a multilocus sequence analysis was carried out using partial gene sequences from the 28S large subunit nrRNA gene (LSU), the internal transcribed spacer (ITS) regions of the nrDNA region, including the 5.8S nrRNA gene, the translation elongation factor 1-alpha (<em>TEF1-α</em>), tryptophan synthase (<em>TS</em>), actin (<em>ACT</em>) and the RNA polymerase II second largest subunit (<em>RPB2</em>), based on a large set of isolates mainly from the CBS collection. Results of the molecular data combined with a detailed morphological study resolved 22 genera in the family, of which 12 are newly described. Additionally, 15 new species and 10 new combinations are proposed. An epitype and neotype are also introduced for <em>Stachylidium bicolor</em> and <em>Plectosphaerella cucumerina</em>, respectively.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"92 ","pages":"Pages 227-286"},"PeriodicalIF":16.5,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.10.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36753761","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":"Phylogeny and genetic diversity of the banana Fusarium wilt pathogen Fusarium oxysporum f. sp. cubense in the Indonesian centre of origin","authors":"N. Maryani ,&nbsp;L. Lombard ,&nbsp;Y.S. Poerba ,&nbsp;S. Subandiyah ,&nbsp;P.W. Crous ,&nbsp;G.H.J. Kema","doi":"10.1016/j.simyco.2018.06.003","DOIUrl":"10.1016/j.simyco.2018.06.003","url":null,"abstract":"<div><p><em>Fusarium oxysporum</em> f. sp. <em>cubense</em> (Foc), the causal agent of Fusarium wilt or Panama disease on banana, is one of the major constraints in banana production worldwide. Indonesia is the centre of origin for wild and cultivated bananas, which likely co-evolved with Foc. This study explored the widest possible genetic diversity of Foc by sampling across Indonesia at 34 geographically and environmentally different locations in 15 provinces at six islands. This resulted in a comprehensive collection of ∼200 isolates from 40 different local banana varieties. Isolates were identified and assessed using sequence analysis of the translation elongation factor-1alpha (<em>tef1</em>), the RNA polymerase II largest subunit (<em>rpb1</em>), and the RNA polymerase II second largest subunit (<em>rpb2</em>). Phylogenetic analyses of these genes allowed the identification of 180 isolates of <em>Fusarium oxysporum</em> f. sp. <em>cubense</em> (Foc), and 20 isolates of the <em>Fusarium fujikuroi</em> species complex (FFSC), the <em>Fusarium incarnatum-equiseti</em> species complex (FIESC), and the <em>Fusarium sambucinum</em> species complex (FSSC). Further analyses, incorporating a worldwide collection of Foc strains, revealed nine independent genetic lineages for Foc, and one novel clade in the <em>Fusarium oxysporum</em> species complex (FOSC). Selected isolates from each lineage were tested on the banana varieties Gros Michel and Cavendish to characterise their pathogenicity profiles. More than 65 % of the isolates were diagnosed as Tropical Race 4 (Foc-TR4) due to their pathogenicity to Cavendish banana, which supports the hypothesis that Foc-TR4 is of Indonesian origin. Nine independent genetic lineages for Foc are formally described in this study. This biodiversity has not been studied since the initial description of Foc in 1919. This study provides a detailed overview of the complexity of Fusarium wilt on banana and its diversity and distribution across Indonesia.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"92 ","pages":"Pages 155-194"},"PeriodicalIF":16.5,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.06.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36408213","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":"Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation","authors":"D. Vu ,&nbsp;M. Groenewald ,&nbsp;M. de Vries ,&nbsp;T. Gehrmann ,&nbsp;B. Stielow ,&nbsp;U. Eberhardt ,&nbsp;A. Al-Hatmi ,&nbsp;J.Z. Groenewald ,&nbsp;G. Cardinali ,&nbsp;J. Houbraken ,&nbsp;T. Boekhout ,&nbsp;P.W. Crous ,&nbsp;V. Robert ,&nbsp;G.J.M. Verkley","doi":"10.1016/j.simyco.2018.05.001","DOIUrl":"10.1016/j.simyco.2018.05.001","url":null,"abstract":"<div><p>Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"92 ","pages":"Pages 135-154"},"PeriodicalIF":16.5,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36268834","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}