Studies in Mycology最新文献

{"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}

{"title":"Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex","authors":"A.R. McTaggart ,&nbsp;T.Y. James ,&nbsp;R.G. Shivas ,&nbsp;A. Drenth ,&nbsp;B.D. Wingfield ,&nbsp;B.A. Summerell ,&nbsp;T.A. Duong","doi":"10.1016/j.simyco.2021.100132","DOIUrl":"10.1016/j.simyco.2021.100132","url":null,"abstract":"<div><p>The <em>Fusarium oxysporum</em> species complex (FOSC) is a group of closely related plant pathogens long-considered strictly clonal, as sexual stages have never been recorded. Several studies have questioned whether recombination occurs in FOSC, and if it occurs its nature and frequency are unknown. We analysed 410 assembled genomes to answer whether FOSC diversified by occasional sexual reproduction interspersed with numerous cycles of asexual reproduction akin to a model of predominant clonal evolution (PCE). We tested the hypothesis that sexual reproduction occurred in the evolutionary history of FOSC by examining the distribution of idiomorphs at the mating locus, phylogenetic conflict and independent measures of recombination from genome-wide SNPs and genes. A phylogenomic dataset of 40 single copy orthologs was used to define structure <em>a priori</em> within FOSC based on genealogical concordance. Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from assembled genomes using a k-mer approach and tested for significant linkage disequilibrium as an indication of PCE. We clone-corrected and tested whether SNPs were randomly associated as an indication of recombination. Our analyses provide evidence for sexual or parasexual reproduction within, but not between, clades of FOSC that diversified from a most recent common ancestor about 500 000 years ago. There was no evidence of substructure based on geography or host that might indicate how clades diversified. Competing evolutionary hypotheses for FOSC are discussed in the context of our results.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"99 ","pages":"Article 100132"},"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/a2/0c/main.PMC8693468.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39696197","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":"Secondary metabolite biosynthetic diversity in the fungal family Hypoxylaceae and Xylaria hypoxylon","authors":"E. Kuhnert ,&nbsp;J.C. Navarro-Muñoz ,&nbsp;K. Becker ,&nbsp;M. Stadler ,&nbsp;J. Collemare ,&nbsp;R.J. Cox","doi":"10.1016/j.simyco.2021.100118","DOIUrl":"10.1016/j.simyco.2021.100118","url":null,"abstract":"<div><p>To date little is known about the genetic background that drives the production and diversification of secondary metabolites in the <em>Hypoxylaceae</em>. With the recent availability of high-quality genome sequences for 13 representative species and one relative (<em>Xylaria hypoxylon</em>) we attempted to survey the diversity of biosynthetic pathways in these organisms to investigate their true potential as secondary metabolite producers. Manual search strategies based on the accumulated knowledge on biosynthesis in fungi enabled us to identify 783 biosynthetic pathways across 14 studied species, the majority of which were arranged in biosynthetic gene clusters (BGC). The similarity of BGCs was analysed with the BiG-SCAPE engine which organised the BGCs into 375 gene cluster families (GCF). Only ten GCFs were conserved across all of these fungi indicating that speciation is accompanied by changes in secondary metabolism. From the known compounds produced by the family members some can be directly correlated with identified BGCs which is highlighted herein by the azaphilone, dihydroxynaphthalene, tropolone, cytochalasan, terrequinone, terphenyl and brasilane pathways giving insights into the evolution and diversification of those compound classes. <em>Vice versa</em>, products of various BGCs can be predicted through homology analysis with known pathways from other fungi as shown for the identified ergot alkaloid, trigazaphilone, curvupallide, viridicatumtoxin and swainsonine BGCs. However, the majority of BGCs had no obvious links to known products from the <em>Hypoxylaceae</em> or other well-studied biosynthetic pathways from fungi. These findings highlight that the number of known compounds strongly underrepresents the biosynthetic potential in these fungi and that a tremendous number of unidentified secondary metabolites is still hidden. Moreover, with increasing numbers of genomes for further <em>Hypoxylaceae</em> species becoming available, the likelihood of revealing new biosynthetic pathways that encode new, potentially useful compounds will significantly improve. Reaching a better understanding of the biology of these producers, and further development of genetic methods for their manipulation, will be crucial to access their treasures.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"99 ","pages":"Article 100118"},"PeriodicalIF":16.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2021.100118","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39419869","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}