Studies in Mycology最新文献

{"title":"New genera and species with chloridium-like morphotype in the <i>Chaetosphaeriales</i> and Vermiculariopsiellales.","authors":"M Réblová, J Nekvindová","doi":"10.3114/sim.2023.106.04","DOIUrl":"10.3114/sim.2023.106.04","url":null,"abstract":"&lt;p&gt;&lt;p&gt;In this study, we investigated the morphological and genetic variability of selected species belonging to the genus &lt;i&gt;Chloridium sensu lato&lt;/i&gt;, some also referred to as chloridium-like asexual morphs and other undescribed morphologically similar fungi. These species do not conform to the revised generic concept and thus necessitate a re-evaluation in terms of taxonomy and phylogeny. The family &lt;i&gt;Chaetosphaeriaceae&lt;/i&gt; (&lt;i&gt;Chaetosphaeriales&lt;/i&gt;) encompasses a wide range of asexual morphotypes, and among them, the simplest form is represented by &lt;i&gt;Chloridium&lt;/i&gt; sect. &lt;i&gt;Chloridium&lt;/i&gt;. The morphological simplicity of the &lt;i&gt;Chloridium&lt;/i&gt; morphotype has historically led to the amalgamation of numerous unrelated species, thereby creating a heterogeneous genus. By conducting phylogenetic reconstruction of four DNA loci and examining a set of 71 strains, including all available ex-type and other non-type strains as well as holotypes and other herbarium material, we were able to gain new insights into the relationships between these taxa. Phylogenetic analyses revealed that the studied species are distantly related to &lt;i&gt;Chloridium&lt;/i&gt; &lt;i&gt;sensu stricto&lt;/i&gt; and can be grouped into two orders in the &lt;i&gt;Sordariomycetes&lt;/i&gt;. Within the &lt;i&gt;Chaetosphaeriales&lt;/i&gt;, they formed nine well-separated genera in four clades, such as &lt;i&gt;Cacumisporium&lt;/i&gt;, &lt;i&gt;Caliciastrum gen. nov.&lt;/i&gt;, &lt;i&gt;Caligospora gen. nov.&lt;/i&gt;, &lt;i&gt;Capillisphaeria gen. nov.&lt;/i&gt;, &lt;i&gt;Curvichaeta&lt;/i&gt;, &lt;i&gt;Fusichloridium&lt;/i&gt;, &lt;i&gt;Geniculoseta gen. nov.&lt;/i&gt;, &lt;i&gt;Papillospora gen. nov.&lt;/i&gt;, and &lt;i&gt;Spicatispora gen. nov.&lt;/i&gt; We also established &lt;i&gt;Chloridiopsiella gen. nov.&lt;/i&gt; and &lt;i&gt;Chloridiopsis gen. nov.&lt;/i&gt; in &lt;i&gt;Vermiculariopsiellales&lt;/i&gt;. Four new species and eight new combinations are proposed in these genera. Our study provides a clearer understanding of the genus &lt;i&gt;Chloridium&lt;/i&gt;, its relationship to other morphologically similar fungi, and a new taxonomic treatment and molecular phylogeny to facilitate their accurate identification and classification in future research. &lt;b&gt;Taxonomic novelties:&lt;/b&gt; &lt;b&gt;New genera:&lt;/b&gt; &lt;i&gt;Caliciastrum&lt;/i&gt; Réblová, &lt;i&gt;Caligospora&lt;/i&gt; Réblová, &lt;i&gt;Capillisphaeria&lt;/i&gt; Réblová, &lt;i&gt;Chloridiopsiella&lt;/i&gt; Réblová, &lt;i&gt;Chloridiopsis&lt;/i&gt; Réblová, &lt;i&gt;Geniculoseta&lt;/i&gt; Réblová, &lt;i&gt;Papillospora&lt;/i&gt; Réblová, &lt;i&gt;Spicatispora&lt;/i&gt; Réblová; &lt;b&gt;New species:&lt;/b&gt; &lt;i&gt;Caliciastrum bicolor&lt;/i&gt; Réblová, &lt;i&gt;Caligospora pannosa&lt;/i&gt; Réblová, &lt;i&gt;Chloridiopsis syzygii&lt;/i&gt; Réblová, &lt;i&gt;Gongromerizella silvana&lt;/i&gt; Réblová; &lt;b&gt;New combinations:&lt;/b&gt; &lt;i&gt;Caligospora dilabens&lt;/i&gt; (Réblová & W. Gams) Réblová, &lt;i&gt;Capillisphaeria&lt;/i&gt; &lt;i&gt;crustacea&lt;/i&gt; (Sacc.) Réblová, &lt;i&gt;Chloridiopsiella preussii&lt;/i&gt; (W. Gams & Hol.-Jech.) Réblová, &lt;i&gt;Chloridiopsis constrictospora&lt;/i&gt; (Crous &lt;i&gt;et al&lt;/i&gt;.) Réblová, &lt;i&gt;Geniculoseta preussii&lt;/i&gt; (W. Gams & Hol.-Jech.) Réblová, &lt;i&gt;Papillospora hebetiseta&lt;/i&gt; (Réblová & W. Gams) Réblová, &lt;i&gt;Spicatispora carpatica&lt;/i&gt; (Hol.-Jech. & Révay) Réblová, &lt;i&gt;Spicatispora fennic","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"1 1","pages":"199-258"},"PeriodicalIF":14.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10825751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69600770","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":"Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of <i>Microbotryomycetes</i>.","authors":"N Schoutteten, A Yurkov, O Leroux, D Haelewaters, D Van Der Straeten, O Miettinen, T Boekhout, D Begerow, A Verbeken","doi":"10.3114/sim.2023.106.02","DOIUrl":"10.3114/sim.2023.106.02","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;&lt;/b&gt; Mycoparasites in &lt;i&gt;Basidiomycota&lt;/i&gt; comprise a diverse group of fungi, both morphologically and phylogenetically. They interact with their hosts through either fusion-interaction or colacosome-interaction. Colacosomes are subcellular structures formed by the mycoparasite at the host-parasite interface, which penetrate the parasite and host cell walls. Previously, these structures were detected in 19 fungal species, usually by means of transmission electron microscopy. Most colacosome-forming species have been assigned to &lt;i&gt;Microbotryomycetes&lt;/i&gt; (&lt;i&gt;Pucciniomycotina&lt;/i&gt;, &lt;i&gt;Basidiomycota&lt;/i&gt;), a highly diverse class, comprising saprobic yeasts, mycoparasites, and phytoparasites. In general, these myco- and phytoparasites are dimorphic organisms, with a parasitic filamentous morph and saprobic yeast morph. We investigated colacosome-forming mycoparasites based on fungarium material, freshly collected specimens, and cultures of yeast morphs. We characterised the micromorphology of filamentous morphs, the physiological characteristics of yeast morphs, and inferred phylogenetic relationships based on DNA sequence data from seven loci. We outline and employ an epifluorescence-based microscopic method to assess the presence and organisation of colacosomes. We describe five new species in the genus &lt;i&gt;Colacogloea&lt;/i&gt;, the novel dimorphic mycoparasite &lt;i&gt;Mycogloiocolax gerardii&lt;/i&gt;, and provide the first report of a sexual, mycoparasitic morph in &lt;i&gt;Colacogloea philyla&lt;/i&gt; and in the genus &lt;i&gt;Slooffia&lt;/i&gt;. We detected colacosomes in eight fungal species, which brings the total number of known colacosome-forming fungi to 27. Finally, we revealed three distinct types of colacosome organisation in &lt;i&gt;Microbotryomycetes&lt;/i&gt;. &lt;b&gt;Taxonomic novelties and typifications:&lt;/b&gt; &lt;b&gt;New family:&lt;/b&gt; &lt;i&gt;Mycogloiocolacaeae&lt;/i&gt; Schoutteten & Yurkov; &lt;b&gt;New genus:&lt;/b&gt; &lt;i&gt;Mycogloiocolax&lt;/i&gt; Schoutteten & Rödel; &lt;b&gt;New species:&lt;/b&gt; &lt;i&gt;Colacogloea bettinae&lt;/i&gt; Schoutteten & Begerow, &lt;i&gt;C. biconidiata&lt;/i&gt; Schoutteten, &lt;i&gt;C. fennica&lt;/i&gt; Schoutteten & Miettinen, &lt;i&gt;C. microspora&lt;/i&gt; Schoutteten, &lt;i&gt;C. universitatis-gandavensis&lt;/i&gt; Schoutteten & Verbeken, &lt;i&gt;Mycogloiocolax gerardii&lt;/i&gt; Schoutteten & Rödel; &lt;b&gt;New combinations:&lt;/b&gt; &lt;i&gt;Slooffia micra&lt;/i&gt; (Bourdot & Galzin) Schoutteten, &lt;i&gt;Fellozyma cerberi&lt;/i&gt; (A.M. Yurkov &lt;i&gt;et al.&lt;/i&gt;) Schoutteten & Yurkov, &lt;i&gt;Fellozyma telluris&lt;/i&gt; (A.M. Yurkov &lt;i&gt;et al.&lt;/i&gt;) Schoutteten & Yurkov; &lt;b&gt;Epitypifications (basionyms):&lt;/b&gt; &lt;i&gt;Achroomyces insignis&lt;/i&gt; Hauerslev, &lt;i&gt;Platygloea micra&lt;/i&gt; Bourdot & Galzin, &lt;i&gt;Platygloea peniophorae&lt;/i&gt; Bourdot & Galzin; &lt;b&gt;Lectotypification (basionym):&lt;/b&gt; &lt;i&gt;Platygloea peniophorae&lt;/i&gt; Bourdot & Galzin &lt;b&gt;Citation:&lt;/b&gt; Schoutteten N, Yurkov A, Leroux O, Haelewaters D, Van Der Straeten D, Miettinen O, Boekhout T, Begerow D, Verbeken A (2023). Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of &lt;i&gt;Microbotryomycetes&lt;/i&gt;. &lt;i&gt;Studies in ","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"106 ","pages":"41-94"},"PeriodicalIF":14.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10825749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651710","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 <i>Claviceps</i> 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.2023.106.01","DOIUrl":"10.3114/sim.2023.106.01","url":null,"abstract":"<p><p><i>Claviceps</i> (<i>Clavicipitaceae</i>, <i>Hypocreales</i>) was erected in 1853, although ergotism had been well-known for a much longer time. By 2000, about 70 taxa had been described in <i>Claviceps</i>, of which eight species and six varieties were based on Japanese type or authentic specimens. Most of these Japanese <i>Claviceps</i> 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 <i>Claviceps</i>. 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, <i>TEF-1α</i>, <i>TUB2</i>, <i>Mcm7</i>, and <i>RPB2</i> revealed the phylogenetic relationships between the Japanese specimens and known <i>Claviceps</i> spp., as well as the presence of biogeographic patterns. Based on the phylogenetic analysis, host range and morphology, we re-evaluated Japanese <i>Claviceps</i> and recognised at least 21 species in Japan. Here we characterised 14 previously described taxa and designated neo-, lecto- and epi-types for <i>C. bothriochloae</i>, <i>C. imperatae</i>, <i>C. litoralis, C. microspora</i>, <i>C. panicoidearum</i> and <i>C. yanagawaensis</i>. Two varieties were elevated to species rank with designated neotypes, <i>i.e.</i> <i>C. agropyri</i> and <i>C. kawatanii</i>. Six new species, <i>C. miscanthicola</i>, <i>C. oplismeni</i>, <i>C. palustris</i>, <i>C. phragmitis</i>, <i>C. sasae</i> and <i>C. tandae</i> were proposed and described. <b>Taxonomic novelties:</b> <b>New species:</b> <i>Claviceps miscanthicola</i> E. Tanaka, <i>Claviceps oplismeni</i> E. Tanaka, <i>Claviceps palustris</i> E. Tanaka, <i>Claviceps phragmitis</i> E. Tanaka, <i>Claviceps sasae</i> E. Tanaka, <i>Claviceps tandae</i> E. Tanaka; <b>New status and combination:</b> <i>Claviceps agropyri</i> (Tanda) E. Tanaka, <i>Claviceps kawatanii</i> (Tanda) E. Tanaka; <b>Typifications (basionyms):</b> <b>Lecto- and epitypification:</b> <i>Claviceps yanagawaensis</i> Togashi; <b>Neotypifications</b>: <i>Claviceps purpurea</i> var. <i>agropyri</i> Tanda, <i>Claviceps bothriochloae</i> Tanda & Y. Muray, <i>Claviceps imperatae</i> Tanda & Kawat., <i>Claviceps microspora</i> var. <i>kawatanii</i> Tanda, <i>Claviceps litoralis</i> Kawat., <i>Claviceps microspora</i> Tanda, <i>Claviceps panicoidearum</i> Tanda & Y. Harada; <b>Resurrection</b>: <i>Claviceps queenslandica</i> Langdon. <b>Citation</b>: Tanaka E, Tanada K, Hosoe T, Shrestha B, Kolařík M, Liu M (2023). In search of lost ergots: phylogenetic re-evaluation of <i>Claviceps</i> species in Japan and their biogeographic patterns revealed. <i>Studies in Mycology</i> <b>106</b>: 1-39. doi: 10.3114/sim.2022.106.01.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"106 ","pages":"1-39"},"PeriodicalIF":14.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10825747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651711","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":"<i>Fusarium</i> diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus.","authors":"S L Han, M M Wang, Z Y Ma, M Raza, P Zhao, J M Liang, M Gao, Y J Li, J W Wang, D M Hu, L Cai","doi":"10.3114/sim.2022.104.02","DOIUrl":"10.3114/sim.2022.104.02","url":null,"abstract":"<p><p><i>Fusarium</i> species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of <i>Fusarium</i> diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 <i>Fusarium</i> strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated <i>Fusarium</i> species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one <i>Fusarium</i> species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the \"narrow\" generic concept of <i>Fusarium</i> (= <i>Gibberella</i>). This study represents one of the most comprehensive surveys of cereal <i>Fusarium</i> diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated <i>Fusarium</i> species, as well as largely clarifies the phylogenetic relationships within the genus. <b>Taxonomic novelties:</b> <b>New species:</b> <i>Fusarium erosum</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium fecundum</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium jinanense</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium mianyangense</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium nothincarnatum</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium planum</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium sanyaense</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium weifangense</i> S.L. Han, M.M. Wang & L. Cai. <b>Citation:</b> Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). <i>Fusarium</i> diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. <i>Studies in Mycology</i> <b>104</b>: 87-148. doi: 10.3114/sim.2022.104.02.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"104 ","pages":"87-148"},"PeriodicalIF":14.1,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10282163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9712358","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":"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}