Studies in Mycology最新文献

{"title":"Taxonomy, phylogeny and identification of <i>Chaetomiaceae</i> with emphasis on thermophilic species.","authors":"X W Wang, P J Han, F Y Bai, A Luo, K Bensch, M Meijer, Kraak B, D Y Han, B D Sun, P W Crous, J Houbraken","doi":"10.3114/sim.2022.101.03","DOIUrl":"10.3114/sim.2022.101.03","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Chaetomiaceae&lt;/i&gt; comprises phenotypically diverse species, which impact biotechnology, the indoor environment and human health. Recent studies showed that most of the traditionally defined genera in &lt;i&gt;Chaetomiaceae&lt;/i&gt; are highly polyphyletic. Many of these morphology-based genera, such as &lt;i&gt;Chaetomium&lt;/i&gt;, &lt;i&gt;Thielavia&lt;/i&gt; and &lt;i&gt;Humicola&lt;/i&gt;, have been redefined using multigene phylogenetic analysis combined with morphology; however, a comprehensive taxonomic overview of the family is lacking. In addition, the phylogenetic relationship of thermophilic &lt;i&gt;Chaetomiaceae&lt;/i&gt; species with non-thermophilic taxa in the family is largely unclear due to limited taxon sampling in previous studies. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of genera and species belonging to &lt;i&gt;Chaetomiaceae&lt;/i&gt;, including an extensive taxon sampling of thermophiles. A multigene phylogenetic analysis based on the ITS (internal transcribed spacers 1 and 2 including the 5.8S nrDNA), LSU (D1/D2 domains of the 28S nrDNA), &lt;i&gt;rpb2&lt;/i&gt; (partial RNA polymerase II second largest subunit gene) and &lt;i&gt;tub2&lt;/i&gt; (β-tubulin gene) sequences was performed on 345 strains representing &lt;i&gt;Chaetomiaceae&lt;/i&gt; and 58 strains of other families in &lt;i&gt;Sordariales&lt;/i&gt;. Divergence times based on the multi-gene phylogeny were estimated as aid to determine the genera in the family. Genera were delimited following the criteria that a genus must be a statistically well-supported monophyletic clade in both the multigene phylogeny and molecular dating analysis, fall within a divergence time of over 27 million years ago, and be supported by ecological preference or phenotypic traits. Based on the results of the phylogeny and molecular dating analyses, combined with morphological characters and temperature-growth characteristics, 50 genera and 275 species are accepted in &lt;i&gt;Chaetomiaceae&lt;/i&gt;. Among them, six new genera, six new species, 45 new combinations and three new names are proposed. The results demonstrate that the thermophilic species fall into seven genera (&lt;i&gt;Melanocarpus&lt;/i&gt;, &lt;i&gt;Mycothermus&lt;/i&gt;, &lt;i&gt;Remersonia&lt;/i&gt;, &lt;i&gt;Thermocarpiscus&lt;/i&gt; &lt;i&gt;gen. nov&lt;/i&gt;., &lt;i&gt;Thermochaetoides&lt;/i&gt; &lt;i&gt;gen. nov&lt;/i&gt;., &lt;i&gt;Thermothelomyces&lt;/i&gt; and &lt;i&gt;Thermothielavioides&lt;/i&gt;). These genera cluster in six separate lineages, suggesting that thermophiles independently evolved at least six times within the family. A list of accepted genera and species in &lt;i&gt;Chaetomiaceae&lt;/i&gt;, together with information on their MycoBank numbers, living ex-type strains and GenBank accession numbers to ITS, LSU, &lt;i&gt;rpb2&lt;/i&gt; and &lt;i&gt;tub2&lt;/i&gt; sequences is provided. Furthermore, we provide suggestions how to describe and identify &lt;i&gt;Chaetomiaceae&lt;/i&gt; species. &lt;b&gt;Taxonomic novelties:&lt;/b&gt; &lt;b&gt;new genera:&lt;/b&gt; &lt;i&gt;Parvomelanocarpus&lt;/i&gt; X.Wei Wang & Houbraken&lt;i&gt;, Pseudohumicola&lt;/i&gt; X.Wei Wang, P.J. Han, F.Y. Bai & Houbraken, &lt;i&gt;Tengochaeta&lt;/i&gt; X.Wei Wang & Houbraken, &lt;i&gt;Thermocarpiscus&lt;/i&gt; X.Wei Wang & Houb","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"121-243"},"PeriodicalIF":14.1,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348346","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":"Species diversity, systematic revision and molecular phylogeny of <i>Ganodermataceae</i> (<i>Polyporales</i>, <i>Basidiomycota</i>) with an emphasis on Chinese collections.","authors":"Y-F Sun,&nbsp;J-H Xing,&nbsp;X-L He,&nbsp;D-M Wu,&nbsp;C-G Song,&nbsp;S Liu,&nbsp;J Vlasák,&nbsp;G Gates,&nbsp;T B Gibertoni,&nbsp;B-K Cui","doi":"10.3114/sim.2022.101.05","DOIUrl":"https://doi.org/10.3114/sim.2022.101.05","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Ganodermataceae&lt;/i&gt; is one of the main families of macrofungi since species in the family are both ecologically and economically important. The double-walled basidiospores with ornamented endospore walls are the characteristic features of &lt;i&gt;Ganodermataceae&lt;/i&gt;. It is a large and complex family; although many studies have focused on &lt;i&gt;Ganodermataceae&lt;/i&gt;, the global diversity, geographic distribution, taxonomy and molecular phylogeny of &lt;i&gt;Ganodermataceae&lt;/i&gt; still remained incompletely understood. In this work, taxonomic and phylogenetic studies on worldwide species of &lt;i&gt;Ganodermataceae&lt;/i&gt; were carried out by morphological examination and molecular phylogenetic analyses inferred from six gene loci including the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the second largest subunit of RNA polymerase II gene (&lt;i&gt;rpb2&lt;/i&gt;), the translation elongation factor 1-α gene (&lt;i&gt;tef1&lt;/i&gt;), the small subunit mitochondrial rRNA gene (mtSSU) and the small subunit nuclear ribosomal RNA gene (nSSU). A total of 1 382 sequences were used in the phylogenetic analyses, of which 817 were newly generated, including 132 sequences of ITS, 139 sequences of nLSU, 83 sequences of &lt;i&gt;rpb2&lt;/i&gt;, 124 sequences of &lt;i&gt;tef1&lt;/i&gt;, 150 sequences of mtSSU and 189 sequences of nSSU. The combined six-gene dataset included sequences from 391 specimens representing 146 taxa from &lt;i&gt;Ganodermataceae&lt;/i&gt;. Based on morphological and phylogenetic analyses, 14 genera were confirmed in &lt;i&gt;Ganodermataceae&lt;/i&gt;: &lt;i&gt;Amauroderma&lt;/i&gt;, &lt;i&gt;Amaurodermellus&lt;/i&gt;, &lt;i&gt;Cristataspora&lt;/i&gt;, &lt;i&gt;Foraminispora&lt;/i&gt;, &lt;i&gt;Furtadoella&lt;/i&gt;, &lt;i&gt;Ganoderma&lt;/i&gt;, &lt;i&gt;Haddowia&lt;/i&gt;, &lt;i&gt;Humphreya&lt;/i&gt;, &lt;i&gt;Magoderna&lt;/i&gt;, &lt;i&gt;Neoganoderma&lt;/i&gt;, &lt;i&gt;Sanguinoderma&lt;/i&gt;, &lt;i&gt;Sinoganoderma&lt;/i&gt;, &lt;i&gt;Tomophagus&lt;/i&gt; and &lt;i&gt;Trachydermella&lt;/i&gt;. Among these genera, &lt;i&gt;Neoganoderma gen. nov.&lt;/i&gt; is proposed for &lt;i&gt;Ganoderma neurosporum&lt;/i&gt;; &lt;i&gt;Sinoganoderma gen. nov.&lt;/i&gt; is proposed for &lt;i&gt;Ganoderma shandongense&lt;/i&gt;; &lt;i&gt;Furtadoella gen. nov.&lt;/i&gt; is proposed to include taxa previously belonging to &lt;i&gt;Furtadoa&lt;/i&gt; since &lt;i&gt;Furtadoa&lt;/i&gt; is a homonym of a plant genus in the &lt;i&gt;Araceae&lt;/i&gt;; &lt;i&gt;Trachydermella gen. nov.&lt;/i&gt; is proposed to include &lt;i&gt;Trachyderma tsunodae&lt;/i&gt; since &lt;i&gt;Trachyderma&lt;/i&gt; is a homonym of a lichen genus in the &lt;i&gt;Pannariaceae&lt;/i&gt;. Twenty-three new species, &lt;i&gt;viz&lt;/i&gt;., &lt;i&gt;Ganoderma acaciicola&lt;/i&gt;, &lt;i&gt;G. acontextum&lt;/i&gt;, &lt;i&gt;G. alpinum&lt;/i&gt;, &lt;i&gt;G. bubalinomarginatum&lt;/i&gt;, &lt;i&gt;G. castaneum&lt;/i&gt;, &lt;i&gt;G. chuxiongense&lt;/i&gt;, &lt;i&gt;G. cocoicola&lt;/i&gt;, &lt;i&gt;G. fallax&lt;/i&gt;, &lt;i&gt;G. guangxiense&lt;/i&gt;, &lt;i&gt;G. puerense&lt;/i&gt;, &lt;i&gt;G. subangustisporum&lt;/i&gt;, &lt;i&gt;G. subellipsoideum&lt;/i&gt;, &lt;i&gt;G. subflexipes&lt;/i&gt;, &lt;i&gt;G. sublobatum&lt;/i&gt;, &lt;i&gt;G. tongshanense&lt;/i&gt;, &lt;i&gt;G. yunlingense&lt;/i&gt;, &lt;i&gt;Haddowia macropora&lt;/i&gt;, &lt;i&gt;Sanguinoderma guangdongense&lt;/i&gt;, &lt;i&gt;Sa. infundibulare&lt;/i&gt;, &lt;i&gt;Sa. longistipitum&lt;/i&gt;, &lt;i&gt;Sa. melanocarpum&lt;/i&gt;, &lt;i&gt;Sa. microsporum&lt;/i&gt; and &lt;i&gt;Sa. tricolor&lt;/i&gt; are described. In addition, another 33 known ","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"287-415"},"PeriodicalIF":16.5,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348348","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 Agaricomycetes","authors":"L. Nagy, P. Vonk, M. Künzler, C. Földi, M. Virágh, R. Ohm, F. Hennicke, B. Bálint, Á. Csernetics, B. Hegedüs, Z. Hou, X. Liu, S. Nan, M. Pareek, N. Sahu, B. Szathmári, T. Varga, H. Wu, X. Yang, Z. Merényi","doi":"10.1101/2021.12.09.471732","DOIUrl":"https://doi.org/10.1101/2021.12.09.471732","url":null,"abstract":"Fruiting bodies of mushroom-forming fungi (Agaricomycetes) 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 tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed 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, defense, 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 1480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, 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 Agaricomycetes. 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.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"104 1","pages":"1 - 85"},"PeriodicalIF":16.5,"publicationDate":"2021-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43463552","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":"Aspergillus fumigatus and aspergillosis: From basics to clinics","authors":"A. Arastehfar ,&nbsp;A. Carvalho ,&nbsp;J. Houbraken ,&nbsp;L. Lombardi ,&nbsp;R. Garcia-Rubio ,&nbsp;J.D. Jenks ,&nbsp;O. Rivero-Menendez ,&nbsp;R. Aljohani ,&nbsp;I.D. Jacobsen ,&nbsp;J. Berman ,&nbsp;N. Osherov ,&nbsp;M.T. Hedayati ,&nbsp;M. Ilkit ,&nbsp;D. Armstrong-James ,&nbsp;T. Gabaldón ,&nbsp;J. Meletiadis ,&nbsp;M. Kostrzewa ,&nbsp;W. Pan ,&nbsp;C. Lass-Flörl ,&nbsp;D.S. Perlin ,&nbsp;M. Hoenigl","doi":"10.1016/j.simyco.2021.100115","DOIUrl":"https://doi.org/10.1016/j.simyco.2021.100115","url":null,"abstract":"<div><p>The airborne fungus <em>Aspergillus fumigatus</em> poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant <em>A</em>. <em>fumigatus</em> isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in <em>CYP</em><em>51A</em> are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type <em>CYP</em><em>51A</em> genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant <em>A</em>. <em>fumigatus</em> isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against <em>A</em>. <em>fumigatus</em>. This review paper comprehensively discusses the current clinical challenges caused by <em>A</em>. <em>fumigatus</em> and provides insights on how to address them.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"100 ","pages":"Article 100115"},"PeriodicalIF":16.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2021.100115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92099345","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":"Trends in the molecular epidemiology and population genetics of emerging Sporothrix species","authors":"J.A. de Carvalho ,&nbsp;M.A. Beale ,&nbsp;F. Hagen ,&nbsp;M.C. Fisher ,&nbsp;R. Kano ,&nbsp;A. Bonifaz ,&nbsp;C. Toriello ,&nbsp;R. Negroni ,&nbsp;R.S. de M. Rego ,&nbsp;I.D.F. Gremião ,&nbsp;S.A. Pereira ,&nbsp;Z.P. de Camargo ,&nbsp;A.M. Rodrigues","doi":"10.1016/j.simyco.2021.100129","DOIUrl":"https://doi.org/10.1016/j.simyco.2021.100129","url":null,"abstract":"&lt;div&gt;&lt;p&gt;&lt;em&gt;Sporothrix&lt;/em&gt; (&lt;em&gt;Ophiostomatales&lt;/em&gt;) comprises species that are pathogenic to humans and other mammals as well as environmental fungi. Developments in molecular phylogeny have changed our perceptions about the epidemiology, host-association, and virulence of &lt;em&gt;Sporothrix&lt;/em&gt;. The classical agent of sporotrichosis, &lt;em&gt;Sporothrix schenckii&lt;/em&gt;, now comprises several species nested in a clinical clade with &lt;em&gt;S. brasiliensis&lt;/em&gt;, &lt;em&gt;S. globosa&lt;/em&gt;, and &lt;em&gt;S. luriei&lt;/em&gt;. To gain a more precise view of outbreaks dynamics, structure, and origin of genetic variation within and among populations of &lt;em&gt;Sporothrix&lt;/em&gt;, we applied three sets of discriminatory AFLP markers (#3 EcoRI-GA/MseI-TT, #5 EcoRI-GA/MseI-AG, and #6 EcoRI-TA/MseI-AA) and mating-type analysis to a large collection of human, animal and environmental isolates spanning the major endemic areas. A total of 451 polymorphic loci were amplified &lt;em&gt;in vitro&lt;/em&gt; from 188 samples, and revealed high polymorphism information content (&lt;em&gt;PIC&lt;/em&gt; = 0.1765–0.2253), marker index (&lt;em&gt;MI&lt;/em&gt; = 0.0001–0.0002), effective multiplex ratio (&lt;em&gt;E&lt;/em&gt; = 15.1720–23.5591), resolving power (&lt;em&gt;Rp&lt;/em&gt; = 26.1075–40.2795), discriminating power (&lt;em&gt;D&lt;/em&gt; = 0.9766–0.9879), expected heterozygosity (&lt;em&gt;H&lt;/em&gt; = 0.1957–0.2588), and mean heterozygosity (&lt;em&gt;H&lt;sub&gt;avp&lt;/sub&gt;&lt;/em&gt; = 0.000007–0.000009), demonstrating the effectiveness of AFLP markers to speciate &lt;em&gt;Sporothrix&lt;/em&gt;. Analysis using the program &lt;span&gt;structure&lt;/span&gt; indicated three genetic clusters matching &lt;em&gt;S. brasiliensis&lt;/em&gt; (population 1), &lt;em&gt;S. schenckii&lt;/em&gt; (population 2), and &lt;em&gt;S. globosa&lt;/em&gt; (population 3), with the presence of patterns of admixture amongst all populations. AMOVA revealed highly structured clusters (PhiPT = 0.458–0.484, &lt;em&gt;P&lt;/em&gt; &lt; 0.0001), with roughly equivalent genetic variability within (46–48 %) and between (52–54 %) populations. Heterothallism was the exclusive mating strategy, and the distributions of &lt;em&gt;MAT1-1&lt;/em&gt; or &lt;em&gt;MAT1-2&lt;/em&gt; idiomorphs were not significantly skewed (1:1 ratio) for &lt;em&gt;S. schenckii&lt;/em&gt; (χ&lt;sup&gt;2&lt;/sup&gt; = 2.522; &lt;em&gt;P&lt;/em&gt; = 0.1122), supporting random mating. In contrast, skewed distributions were found for &lt;em&gt;S. globosa&lt;/em&gt; (χ&lt;sup&gt;2&lt;/sup&gt; = 9.529; &lt;em&gt;P&lt;/em&gt; = 0.0020) with a predominance of &lt;em&gt;MAT1-1&lt;/em&gt; isolates, and regional differences were highlighted for &lt;em&gt;S. brasiliensis&lt;/em&gt; with the overwhelming occurrence of &lt;em&gt;MAT1-2&lt;/em&gt; in Rio de Janeiro (χ&lt;sup&gt;2&lt;/sup&gt; = 14.222; &lt;em&gt;P&lt;/em&gt; = 0.0002) and Pernambuco (χ&lt;sup&gt;2&lt;/sup&gt; = 7.364; &lt;em&gt;P&lt;/em&gt; = 0.0067), in comparison to a higher prevalence of &lt;em&gt;MAT1-1&lt;/em&gt; in the Rio Grande do Sul (χ&lt;sup&gt;2&lt;/sup&gt; = 7.364; &lt;em&gt;P&lt;/em&gt; = 0.0067). Epidemiological trends reveal the geographic expansion of cat-transmitted sporotrichosis due to &lt;em&gt;S. brasiliensis&lt;/em&gt; via founder effect. These data support Rio de Janeiro as the centre of origin that has led to the spread of this disease to other regions in Brazil","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"100 ","pages":"Article 100129"},"PeriodicalIF":16.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0166061621000166/pdfft?md5=2d66cf749c8b6b116da997ac6b51cd53&pid=1-s2.0-S0166061621000166-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92066454","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":"Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy","authors":"A. Arastehfar ,&nbsp;M. Marcet-Houben ,&nbsp;F. Daneshnia ,&nbsp;S.J. Taj-Aldeen ,&nbsp;D. Batra ,&nbsp;S.R. Lockhart ,&nbsp;E. Shor ,&nbsp;T. Gabaldón ,&nbsp;D.S. Perlin","doi":"10.1016/j.simyco.2021.100133","DOIUrl":"https://doi.org/10.1016/j.simyco.2021.100133","url":null,"abstract":"<div><p><em>Candida glabrata</em> is the second leading cause of candidemia in many countries and is one of the most concerning yeast species of nosocomial importance due to its increasing rate of antifungal drug resistance and emerging multidrug-resistant isolates. Application of multilocus sequence typing (MLST) to clinical <em>C. glabrata</em> isolates revealed an association of certain sequence types (STs) with drug resistance and mortality. The current <em>C. glabrata</em> MLST scheme is based on single nucleotide polymorphisms (SNPs) at six loci and is therefore relatively laborious and costly. Furthermore, only a few high-quality <em>C. glabrata</em> reference genomes are available, limiting rapid analysis of clinical isolates by whole genome sequencing. In this study we provide long-read based assemblies for seven additional clinical strains belonging to three different STs and use this information to simplify the <em>C. glabrata</em> MLST scheme. Specifically, a comparison of these genomes identified highly polymorphic loci (HPL) defined by frequent insertions and deletions (indels), two of which proved to be highly resolutive for ST. When challenged with 53 additional isolates, a combination of <em>TRP1</em> (a component of the current MLST scheme) with either of the two HPL fully recapitulated ST identification. Therefore, our comparative genomic analysis identified a new typing approach combining SNPs and indels and based on only two loci, thus significantly simplifying ST identification in <em>C. glabrata</em>. Because typing tools are instrumental in addressing numerous clinical and biological questions, our new MLST scheme can be used for high throughput typing of <em>C. glabrata</em> in clinical and research settings.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"100 ","pages":"Article 100133"},"PeriodicalIF":16.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0166061621000208/pdfft?md5=7511e85e8764997b464763fdf771e7f5&pid=1-s2.0-S0166061621000208-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92066237","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":"Exploring genetic diversity, population structure, and phylogeography in Paracoccidioides species using AFLP markers","authors":"T.N. Roberto ,&nbsp;J.A. de Carvalho ,&nbsp;M.A. Beale ,&nbsp;F. Hagen ,&nbsp;M.C. Fisher ,&nbsp;R.C. Hahn ,&nbsp;Z.P. de Camargo ,&nbsp;A.M. Rodrigues","doi":"10.1016/j.simyco.2021.100131","DOIUrl":"https://doi.org/10.1016/j.simyco.2021.100131","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation of &lt;em&gt;Paracoccidioides&lt;/em&gt; propagules from the environment. The main agents include members of the &lt;em&gt;P. brasiliensis&lt;/em&gt; complex (phylogenetically-defined species S1, PS2, PS3, and PS4) and &lt;em&gt;P. lutzii&lt;/em&gt;. DNA-sequencing of protein-coding loci (e.g., &lt;em&gt;GP43&lt;/em&gt;, &lt;em&gt;ARF&lt;/em&gt;, and &lt;em&gt;TUB1&lt;/em&gt;) is the reference method for recognizing &lt;em&gt;Paracoccidioides&lt;/em&gt; species due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity within &lt;em&gt;Paracoccidioides&lt;/em&gt;. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotyping &lt;em&gt;Paracoccidioides&lt;/em&gt; species. The bioinformatic analysis generated 144 &lt;em&gt;in silico&lt;/em&gt; AFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC/MseI-CT and #2 EcoRI-AT/MseI-CT). The combinations #1 and #2 were used &lt;em&gt;in vitro&lt;/em&gt; to genotype 165 &lt;em&gt;Paracoccidioides&lt;/em&gt; isolates recovered from across a vast area of South America. Considering the overall scored AFLP markers &lt;em&gt;in vitro&lt;/em&gt; (67–87 fragments), the values of polymorphism information content (&lt;em&gt;PIC&lt;/em&gt; = 0.3345–0.3456), marker index (&lt;em&gt;MI&lt;/em&gt; = 0.0018), effective multiplex ratio (&lt;em&gt;E&lt;/em&gt; = 44.6788–60.3818), resolving power (&lt;em&gt;Rp&lt;/em&gt; = 22.3152–34.3152), discriminating power (&lt;em&gt;D&lt;/em&gt; = 0.5183–0.5553), expected heterozygosity (&lt;em&gt;H&lt;/em&gt; = 0.4247–0.4443), and mean heterozygosity (&lt;em&gt;H&lt;/em&gt;&lt;sub&gt;&lt;em&gt;avp&lt;/em&gt;&lt;/sub&gt; = 0.00002–0.00004), demonstrated the utility of AFLP markers to speciate &lt;em&gt;Paracoccidioides&lt;/em&gt; and to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability among &lt;em&gt;P. brasiliensis&lt;/em&gt; complex and &lt;em&gt;P. lutzii&lt;/em&gt; (PhiPT = 0.651–0.658, &lt;em&gt;P&lt;/em&gt; &lt; 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions of &lt;em&gt;MAT1-1&lt;/em&gt; or &lt;em&gt;MAT1-2&lt;/em&gt; idiomorphs were not significantly skewed (1:1 ratio) for &lt;em&gt;P. brasiliensis s. str.&lt;/em&gt; (χ&lt;sup&gt;2&lt;/sup&gt; = 1.025; &lt;em&gt;P&lt;/em&gt; = 0.3113), &lt;em&gt;P. venezuelensis&lt;/em&gt; (χ&lt;sup&gt;2&lt;/sup&gt; = 0.692; &lt;em&gt;P&lt;/em&gt; = 0.4054), and &lt;em&gt;P. lutzii&lt;/em&gt; (χ&lt;sup&gt;2&lt;/sup&gt; = 0.027; &lt;em&gt;P&lt;/em&gt; = 0.8694), supporting random mating within each species. In contrast, skewed distributions were found for &lt;em&gt;P. americana&lt;/em&gt; (χ&lt;sup&gt;2&lt;/sup&gt; = 8.909; &lt;em&gt;P&lt;/em&gt; = 0.0028) and &lt;em&gt;P. restrepiensis&lt;/em&gt; (χ&lt;sup&gt;2&lt;/sup&gt; = 4.571; &lt;em&gt;P&lt;/em&gt; = 0.0325) with a preponderance of &lt;em&gt;MAT1-1&lt;/em&gt;. Geographical distributions confirmed that &lt;em&gt;P. americana&lt;/em&gt;, &lt;em&gt;P. restrepiensis&lt;/em&gt;, and &lt;em&gt;P. lutzii&lt;/em&gt; are more widespread than previously thought. &lt;em&gt;P. brasiliensis s. str.&lt;/em&gt; is by far the most widely occurring lineage ","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"100 ","pages":"Article 100131"},"PeriodicalIF":16.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S016606162100018X/pdfft?md5=100158edc53f37ee6facfac887aad254&pid=1-s2.0-S016606162100018X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92066455","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":"Revision of Cerinomyces (Dacrymycetes, Basidiomycota) with notes on morphologically and historically related taxa","authors":"A. Savchenko ,&nbsp;J.C. Zamora ,&nbsp;T. Shirouzu ,&nbsp;V. Spirin ,&nbsp;V. Malysheva ,&nbsp;U. Kõljalg ,&nbsp;O. Miettinen","doi":"10.1016/j.simyco.2021.100117","DOIUrl":"10.1016/j.simyco.2021.100117","url":null,"abstract":"<div><p><em>Cerinomyces (Dacrymycetes</em>, <em>Basidiomycota</em>) is a genus traditionally defined by corticioid basidiocarps, in contrast to the rest of the class, which is characterized by gelatinous ones. In the traditional circumscription the genus is polyphyletic, and the monotypic family <em>Cerinomycetaceae</em> is paraphyletic. Aiming for a more concise delimitation, we revise <em>Cerinomyces s.l.</em> with a novel phylogeny based on sequences of nrDNA (SSU, ITS, LSU) and protein-coding genes (RPB1, RPB2, TEF1-α)<em>.</em> We establish that monophyletic <em>Cerinomyces s.s.</em> is best characterized not by the corticioid morphology, but by a combination of traits: hyphal clamps, predominantly aseptate thin-walled basidiospores, and low content of carotenoid pigments. In our updated definition, <em>Cerinomyces s.s.</em> encompasses five well-supported phylogenetic clades divided into two morphological groups: (i-iii) taxa with arid corticioid basidiocarps, including the generic type <em>C. pallidus</em>; and (iv-v) newly introduced members with gelatinous basidiocarps, like <em>Dacrymyces enatus</em> and <em>D. tortus</em>. The remaining corticioid species of <em>Cerinomyces s.l.</em> are morphologically distinct and belong to the <em>Dacrymycetaceae</em>: our analysis places the carotenoid-rich <em>Cerinomyces canadensis</em> close to <em>Femsjonia</em>, and we transfer the clamps-lacking <em>C. grandinioides</em> group to <em>Dacrymyces.</em> In addition, we address genera related to <em>Cerinomyces s.l.</em> historically and morphologically, such as <em>Ceracea</em>, <em>Dacryonaema</em> and <em>Unilacryma</em>. Overall, we describe twenty-four new species and propose nine new combinations in both <em>Cerinomycetaceae</em> and <em>Dacrymycetaceae</em>.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"99 ","pages":"Article 100117"},"PeriodicalIF":16.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8645972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39746216","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":"Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species","authors":"F. Sklenář ,&nbsp;Ž. Jurjević ,&nbsp;J. Houbraken ,&nbsp;M. Kolařík ,&nbsp;M.C. Arendrup ,&nbsp;K.M. Jørgensen ,&nbsp;J.P.Z. Siqueira ,&nbsp;J. Gené ,&nbsp;T. Yaguchi ,&nbsp;C.N. Ezekiel ,&nbsp;C. Silva Pereira ,&nbsp;V. Hubka","doi":"10.1016/j.simyco.2021.100120","DOIUrl":"10.1016/j.simyco.2021.100120","url":null,"abstract":"<div><p>Since the last revision in 2015, the taxonomy of section <em>Flavipedes</em> evolved rapidly along with the availability of new species delimitation techniques. This study aims to re-evaluate the species boundaries of section <em>Flavipedes</em> members using modern delimitation methods applied to an extended set of strains (n = 90) collected from various environments. The analysis used DNA sequences of three house-keeping genes (<em>benA</em>, <em>CaM</em>, <em>RPB2</em>) and consisted of two steps: application of several single-locus (GMYC, bGMYC, PTP, bPTP) and multi-locus (STACEY) species delimitation methods to sort the isolates into putative species, which were subsequently validated using DELINEATE software that was applied for the first time in fungal taxonomy. As a result, four new species are introduced, <em>i.e.</em> <em>A. alboluteus</em>, <em>A. alboviridis</em>, <em>A. inusitatus</em> and <em>A. lanuginosus</em>, and <em>A. capensis</em> is synonymized with <em>A. iizukae</em>. Phenotypic analyses were performed for the new species and their relatives, and the results showed that the growth parameters at different temperatures and colonies characteristics were useful for differentiation of these taxa. The revised section harbors 18 species, most of them are known from soil. However, the most common species from the section are ecologically diverse, occurring in the indoor environment (six species), clinical samples (five species), food and feed (four species), droppings (four species) and other less common substrates/environments. Due to the occurrence of section <em>Flavipedes</em> species in the clinical material/hospital environment, we also evaluated the susceptibility of 67 strains to six antifungals (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, terbinafine) using the reference EUCAST method. These results showed some potentially clinically relevant differences in susceptibility between species. For example, MICs higher than those observed for <em>A. fumigatus</em> wild-type were found for both triazoles and amphotericin B for <em>A. ardalensis, A. iizukae,</em> and <em>A. spelaeus</em> whereas <em>A. lanuginosus, A. luppiae, A. movilensis, A. neoflavipes, A. olivimuriae</em> and <em>A. suttoniae</em> were comparable to or more susceptible as <em>A. fumigatus</em>. Finally, terbinafine was <em>in vitro</em> active against all species except <em>A. alboviridis</em>.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"99 ","pages":"Article 100120"},"PeriodicalIF":16.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6f/90/main.PMC8688885.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39800411","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 phylogenetic overview of the Hydnaceae (Cantharellales, Basidiomycota) with new taxa from China","authors":"Ting Cao ,&nbsp;Ya-Ping Hu ,&nbsp;Jia-Rui Yu ,&nbsp;Tie-Zheng Wei ,&nbsp;Hai-Sheng Yuan","doi":"10.1016/j.simyco.2021.100121","DOIUrl":"10.1016/j.simyco.2021.100121","url":null,"abstract":"&lt;div&gt;&lt;p&gt;The family &lt;em&gt;Hydnaceae&lt;/em&gt; (&lt;em&gt;Cantharellales&lt;/em&gt;, &lt;em&gt;Basidiomycota&lt;/em&gt;) is a group of fungi found worldwide which exhibit stichic nuclear division. The group is highly diverse in morphology, ecology, and phylogeny, and includes some edible species which are popular all over the world. Traditionally, &lt;em&gt;Hydnaceae&lt;/em&gt; together with &lt;em&gt;Cantharellaceae&lt;/em&gt;, &lt;em&gt;Clavulinaceae&lt;/em&gt; and &lt;em&gt;Sistotremataceae&lt;/em&gt; are four families in the &lt;em&gt;Cantharellales.&lt;/em&gt; The four families were combined and redefined as “&lt;em&gt;Hydnaceae&lt;/em&gt;”, however, a comprehensive phylogeny based on multiple-marker dataset for the entire &lt;em&gt;Hydnaceae sensu stricto&lt;/em&gt; is still lacking and the delimitation is also unclear. We inferred Maximum Likelihood and Bayesian phylogenies for the family &lt;em&gt;Hydnaceae&lt;/em&gt; from the data of five DNA regions: the large subunit of nuclear ribosomal RNA gene (nLSU), the internal transcribed spacer regions (ITS), the mitochondrial small subunit rDNA gene (mtSSU), the second largest subunit of RNA polymerase II (&lt;em&gt;RPB2&lt;/em&gt;) and the translation elongation factor 1-alpha gene (&lt;em&gt;TEF1&lt;/em&gt;). We also produced three more phylogenetic trees for &lt;em&gt;Cantharellus&lt;/em&gt; based on 5.8S, nLSU, mtSSU, &lt;em&gt;RPB2&lt;/em&gt; and &lt;em&gt;TEF1&lt;/em&gt;, &lt;em&gt;Craterellus&lt;/em&gt; and &lt;em&gt;Hydnum&lt;/em&gt; both based on the combined nLSU and ITS. This study has reproduced the status of &lt;em&gt;Hydnaceae&lt;/em&gt; in the order &lt;em&gt;Cantharellales&lt;/em&gt;, and phylogenetically confirmed seventeen genera in &lt;em&gt;Hydnaceae.&lt;/em&gt; Twenty nine new taxa or synonyms are described, revealed, proposed, or reported, including eight new subgenera (&lt;em&gt;Cantharellus&lt;/em&gt; subgenus &lt;em&gt;Magnus&lt;/em&gt;, &lt;em&gt;Craterellus&lt;/em&gt; subgenus &lt;em&gt;Cariosi&lt;/em&gt;, subg. &lt;em&gt;Craterellus&lt;/em&gt;, subg. &lt;em&gt;Imperforati&lt;/em&gt;, subg. &lt;em&gt;Lamelles&lt;/em&gt;, subg. &lt;em&gt;Longibasidiosi&lt;/em&gt;, subg. &lt;em&gt;Ovoidei&lt;/em&gt;, and &lt;em&gt;Hydnum&lt;/em&gt; subgenus &lt;em&gt;Brevispina&lt;/em&gt;); seventeen new species (&lt;em&gt;Ca&lt;/em&gt;. &lt;em&gt;laevihymeninus&lt;/em&gt;, &lt;em&gt;Ca&lt;/em&gt;. &lt;em&gt;magnus&lt;/em&gt;, &lt;em&gt;Ca&lt;/em&gt;. &lt;em&gt;subminor&lt;/em&gt;, &lt;em&gt;Cr&lt;/em&gt;. &lt;em&gt;badiogriseus&lt;/em&gt;, &lt;em&gt;Cr&lt;/em&gt;. &lt;em&gt;croceialbus&lt;/em&gt;, &lt;em&gt;Cr&lt;/em&gt;. &lt;em&gt;macrosporus&lt;/em&gt;, &lt;em&gt;Cr&lt;/em&gt;. &lt;em&gt;squamatus&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;brevispinum&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;flabellatum&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;flavidocanum&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;longibasidium&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;pallidocroceum&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;pallidomarginatum&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;sphaericum&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;tangerinum&lt;/em&gt;, &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;tenuistipitum&lt;/em&gt; and &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;ventricosum&lt;/em&gt;); two synonyms (&lt;em&gt;Ca&lt;/em&gt;. &lt;em&gt;anzutake&lt;/em&gt; and &lt;em&gt;Ca&lt;/em&gt;. &lt;em&gt;tuberculosporus&lt;/em&gt; as &lt;em&gt;Ca&lt;/em&gt;. &lt;em&gt;yunnanensis&lt;/em&gt;), and two newly recorded species (&lt;em&gt;H&lt;/em&gt;. &lt;em&gt;albomagnum&lt;/em&gt; and &lt;em&gt;H&lt;/em&gt;. &lt;em&gt;minum&lt;/em&gt;). The distinguishing characters of the new species and subgenera as well as their allied taxa are discussed in the notes which follow them. The delimitation and diversity in morphology, ecology, and phylogeny of &lt;em&gt;Hydnaceae&lt;/em&gt; is discussed. Notes","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"99 ","pages":"Article 100121"},"PeriodicalIF":16.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/17/9d/main.PMC8717575.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39701943","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}