Studies in Mycology最新文献

{"title":"Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli","authors":"M.R. Mäkelä ,&nbsp;M. DiFalco ,&nbsp;E. McDonnell ,&nbsp;T.T.M. Nguyen ,&nbsp;A. Wiebenga ,&nbsp;K. Hildén ,&nbsp;M. Peng ,&nbsp;I.V. Grigoriev ,&nbsp;A. Tsang ,&nbsp;R.P. de Vries","doi":"10.1016/j.simyco.2018.09.001","DOIUrl":"10.1016/j.simyco.2018.09.001","url":null,"abstract":"<div><p>We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse <em>Aspergillus</em> species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is <em>A. clavatus</em> where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section <em>Nigri</em>, <em>A. aculeatus, A. nidulans</em> and <em>A. terreus</em>, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"91 ","pages":"Pages 79-99"},"PeriodicalIF":16.5,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36715610","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":"Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance","authors":"T. Emri ,&nbsp;K. Antal ,&nbsp;R. Riley ,&nbsp;Z. Karányi ,&nbsp;M. Miskei ,&nbsp;E. Orosz ,&nbsp;S.E. Baker ,&nbsp;A. Wiebenga ,&nbsp;R.P. de Vries ,&nbsp;I. Pócsi","doi":"10.1016/j.simyco.2018.10.003","DOIUrl":"10.1016/j.simyco.2018.10.003","url":null,"abstract":"<div><p>The contribution of stress protein duplication and deletion events to the evolution of the Aspergilli was studied. We performed a large-scale homology analysis of stress proteins and generated and analysed three stress defence system models based on <em>Saccharomyces cerevisiae</em>, <em>Schizosaccharomyces pombe</em> and <em>Aspergillus nidulans</em>. Although both yeast-based and <em>A. nidulans</em>-based models were suitable to trace evolutionary changes, the <em>A. nidulans</em>-based model performed better in mapping stress protein radiations. The strong Mantel correlation found between the positions of species in the phylogenetic tree on the one hand and either in the <em>A. nidulans</em>-based or <em>S. cerevisiae</em>-based models on the other hand demonstrated that stress protein expansions and reductions contributed significantly to the evolution of the Aspergilli. Interestingly, stress tolerance attributes correlated well with the number of orthologs only for a few stress proteins. Notable examples are Ftr1 iron permease and Fet3 ferro-O₂-oxidoreductase, elements of the reductive iron assimilation pathway, in the <em>S. cerevisiae</em>-based model, as well as MpkC, a HogA-like mitogen activated protein kinase in the <em>A. nidulans</em>-based model. In the case of the iron assimilation proteins, the number of orthologs showed a positive correlation with H₂O₂-induced stress tolerance while the number of MpkC orthologs correlated positively with Congo Red induced cell wall stress, sorbitol induced osmotic stress and H₂O₂ induced oxidative stress tolerances. For most stress proteins, changes in the number of orthologs did not correlate well with any stress tolerance attributes. As a consequence, stress tolerance patterns of the studied Aspergilli did not correlate with either the sets of stress response proteins in general or with the phylogeny of the species studied. These observations suggest that stress protein duplication and deletion events significantly contributed to the evolution of stress tolerance attributes of Aspergilli. In contrast, there are other processes, which may counterbalance the effects of stress gene duplications or deletions including (i) alterations in the structures of stress proteins leading to changes in their biological activities, (ii) varying biosynthesis of stress proteins, (iii) rewiring stress response regulatory networks or even (iv) acquiring new stress response genes by horizontal gene transfer. All these multilevel changes are indispensable for the successful adaptation of filamentous fungi to altering environmental conditions, especially when these organisms are entering new ecological niches.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"91 ","pages":"Pages 23-36"},"PeriodicalIF":16.5,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.10.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36675899","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":"Evolution of asexual and sexual reproduction in the aspergilli","authors":"M. Ojeda-López ,&nbsp;W. Chen ,&nbsp;C.E. Eagle ,&nbsp;G. Gutiérrez ,&nbsp;W.L. Jia ,&nbsp;S.S. Swilaiman ,&nbsp;Z. Huang ,&nbsp;H.-S. Park ,&nbsp;J.-H. Yu ,&nbsp;D. Cánovas ,&nbsp;P.S. Dyer","doi":"10.1016/j.simyco.2018.10.002","DOIUrl":"10.1016/j.simyco.2018.10.002","url":null,"abstract":"&lt;div&gt;&lt;p&gt;&lt;em&gt;Aspergillus nidulans&lt;/em&gt; has long-been used as a model organism to gain insights into the genetic basis of asexual and sexual developmental processes both in other members of the genus &lt;em&gt;Aspergillus&lt;/em&gt;, and filamentous fungi in general. Paradigms have been established concerning the regulatory mechanisms of conidial development. However, recent studies have shown considerable genome divergence in the fungal kingdom, questioning the general applicability of findings from &lt;em&gt;Aspergillus&lt;/em&gt;, and certain longstanding evolutionary theories have been questioned. The phylogenetic distribution of key regulatory elements of asexual reproduction in &lt;em&gt;A. nidulans&lt;/em&gt; was investigated in a broad taxonomic range of fungi. This revealed that some proteins were well conserved in the &lt;em&gt;Pezizomycotina&lt;/em&gt; (&lt;em&gt;e.g.&lt;/em&gt; AbaA, FlbA, FluG, NsdD, MedA, and some velvet proteins), suggesting similar developmental roles. However, other elements (&lt;em&gt;e.g.&lt;/em&gt; BrlA) had a more restricted distribution solely in the &lt;em&gt;Eurotiomycetes&lt;/em&gt;, and it appears that the genetic control of sporulation seems to be more complex in the aspergilli than in some other taxonomic groups of the &lt;em&gt;Pezizomycotina&lt;/em&gt;. The evolution of the velvet protein family is discussed based on the history of expansion and contraction events in the early divergent fungi. Heterologous expression of the &lt;em&gt;A. nidulans abaA&lt;/em&gt; gene in &lt;em&gt;Monascus ruber&lt;/em&gt; failed to induce development of complete conidiophores as seen in the aspergilli, but did result in increased conidial production. The absence of many components of the asexual developmental pathway from members of the &lt;em&gt;Saccharomycotina&lt;/em&gt; supports the hypothesis that differences in the complexity of their spore formation is due in part to the increased diversity of the sporulation machinery evident in the &lt;em&gt;Pezizomycotina&lt;/em&gt;. Investigations were also made into the evolution of sex and sexuality in the aspergilli. &lt;em&gt;MAT&lt;/em&gt; loci were identified from the heterothallic &lt;em&gt;Aspergillus&lt;/em&gt; (&lt;em&gt;Emericella&lt;/em&gt;) &lt;em&gt;heterothallicus&lt;/em&gt; and &lt;em&gt;Aspergillus&lt;/em&gt; (&lt;em&gt;Neosartorya&lt;/em&gt;) &lt;em&gt;fennelliae&lt;/em&gt; and the homothallic &lt;em&gt;Aspergillus pseudoglaucus&lt;/em&gt; (=&lt;em&gt;Eurotium repens&lt;/em&gt;). A consistent architecture of the &lt;em&gt;MAT&lt;/em&gt; locus was seen in these and other heterothallic aspergilli whereas much variation was seen in the arrangement of &lt;em&gt;MAT&lt;/em&gt; loci in homothallic aspergilli. This suggested that it is most likely that the common ancestor of the aspergilli exhibited a heterothallic breeding system. Finally, the supposed prevalence of asexuality in the aspergilli was examined. Investigations were made using &lt;em&gt;A. clavatus&lt;/em&gt; as a representative ‘asexual’ species. It was possible to induce a sexual cycle in &lt;em&gt;A. clavatus&lt;/em&gt; given the correct &lt;em&gt;MAT1-1&lt;/em&gt; and &lt;em&gt;MAT1-2&lt;/em&gt; partners and environmental conditions, with recombination confirmed utilising molecular markers. This indicated that sexua","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"91 ","pages":"Pages 37-59"},"PeriodicalIF":16.5,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.10.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36676317","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":"The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi","authors":"M.V. Aguilar-Pontes ,&nbsp;J. Brandl ,&nbsp;E. McDonnell ,&nbsp;K. Strasser ,&nbsp;T.T.M. Nguyen ,&nbsp;R. Riley ,&nbsp;S. Mondo ,&nbsp;A. Salamov ,&nbsp;J.L. Nybo ,&nbsp;T.C. Vesth ,&nbsp;I.V. Grigoriev ,&nbsp;M.R. Andersen ,&nbsp;A. Tsang ,&nbsp;R.P. de Vries","doi":"10.1016/j.simyco.2018.10.001","DOIUrl":"10.1016/j.simyco.2018.10.001","url":null,"abstract":"<div><p>The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism.</p><p>Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"91 ","pages":"Pages 61-78"},"PeriodicalIF":16.5,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.10.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36676789","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":"Coelomycetous Dothideomycetes with emphasis on the families Cucurbitariaceae and Didymellaceae","authors":"N. Valenzuela-Lopez ,&nbsp;J.F. Cano-Lira ,&nbsp;J. Guarro ,&nbsp;D.A. Sutton ,&nbsp;N. Wiederhold ,&nbsp;P.W. Crous ,&nbsp;A.M. Stchigel","doi":"10.1016/j.simyco.2017.11.003","DOIUrl":"10.1016/j.simyco.2017.11.003","url":null,"abstract":"<div><p>The taxonomy of the coelomycetes has undergone dramatic changes in recent years, but remains controversial due to the high number of taxa involved, their poor morphological differentiation, the rare occurrence of the sexual morphs, and rapid loss of fertility <em>in vitro</em>. In the present study, we revisited the families <em>Cucurbitariaceae</em> and <em>Didymellaceae</em> (<em>Pleosporales, Dothideomycetes</em>), which include numerous plant pathogens, endophytic species associated with a wide host range, and saprobes. The taxonomy of two of the most relevant genera, i.e. <em>Phoma</em> and <em>Pyrenochaeta</em>, remains ambiguous after several phylogenetic studies, and needs further revision. We have studied a total of 143 strains of coelomycetes from clinical or environmental origin, by combining the LSU, ITS, <em>tub</em>2 and <em>rpb</em>2 sequences for a multi-locus analysis and a detailed morphological comparison. The resulting phylogenetic tree revealed that some fungi previously considered as members of <em>Cucurbitariaceae</em> represented five different families, and four of them, <em>Neopyrenochaetaceae</em>, <em>Parapyrenochaetaceae</em>, <em>Pseudopyrenochaetaceae</em> and <em>Pyrenochaetopsidaceae</em>, are proposed here as new. Furthermore, 13 new genera, 28 new species, and 20 new combinations are proposed within the <em>Pleosporineae</em>. Moreover, four new typifications are introduced to stabilise the taxonomy of these fungi.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"90 ","pages":"Pages 1-69"},"PeriodicalIF":16.5,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2017.11.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35668821","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":"Zombie-ant fungi across continents: 15 new species and new combinations within Ophiocordyceps. I. Myrmecophilous hirsutelloid species","authors":"J.P.M. Araújo ,&nbsp;H.C. Evans ,&nbsp;R. Kepler ,&nbsp;D.P. Hughes","doi":"10.1016/j.simyco.2017.12.002","DOIUrl":"10.1016/j.simyco.2017.12.002","url":null,"abstract":"<div><p><em>Ophiocordyceps</em> species infecting ants – the so-called zombie-ant fungi – comprise one of the most intriguing and fascinating relationships between microbes and animals. They are widespread within tropical forests worldwide, with relatively few reports from temperate ecosystems. These pathogens possess the ability to manipulate host behaviour in order to increase their own fitness. Depending on the fungal species involved the infected ants are manipulated either to leave the nest to ascend understorey shrubs, to die biting onto vegetation, or descend from the canopy to die at the base of trees. Experimental evidence has demonstrated that the behavioural change aids spore dispersal and thus increases the chances of infection, because of the existing behavioural immunity expressed inside ant colonies that limits fungal development and transmission. Despite their undoubted importance for ecosystem functioning, these fungal pathogens are still poorly documented, especially regarding their diversity, ecology and evolutionary relationships. Here, we describe 15 new species of <em>Ophiocordyceps</em> with hirsutella-like asexual morphs that exclusively infect ants. These form a monophyletic group that we identified in this study as myrmecophilous hirsutelloid species. We also propose new combinations for species previously described as varieties and provide for the first time important morphological and ecological information. The species proposed herein were collected in Brazil, Colombia, USA, Australia and Japan. All species could readily be separated using classic taxonomic criteria, in particular ascospore and asexual morphology.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"90 ","pages":"Pages 119-160"},"PeriodicalIF":16.5,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2017.12.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36229939","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":"Resolving the Lophiostoma bipolare complex: Generic delimitations within Lophiostomataceae","authors":"A. Hashimoto ,&nbsp;K. Hirayama ,&nbsp;H. Takahashi ,&nbsp;M. Matsumura ,&nbsp;G. Okada ,&nbsp;C.Y. Chen ,&nbsp;J.W. Huang ,&nbsp;M. Kakishima ,&nbsp;T. Ono ,&nbsp;K. Tanaka","doi":"10.1016/j.simyco.2018.03.001","DOIUrl":"10.1016/j.simyco.2018.03.001","url":null,"abstract":"&lt;div&gt;&lt;p&gt;&lt;em&gt;Lophiostoma bipolare&lt;/em&gt; was taxonomically revised based on the morphological observations and phylogenetic analyses of molecular data from nuclear rDNA SSU-ITS-LSU, &lt;em&gt;TUB&lt;/em&gt;, &lt;em&gt;tef1&lt;/em&gt;, and &lt;em&gt;rpb2&lt;/em&gt; genes. Twenty-nine strains were morphologically similar to &lt;em&gt;Lo&lt;/em&gt;. &lt;em&gt;bipolare&lt;/em&gt;. A total of 174 sequences were generated from the &lt;em&gt;Lo&lt;/em&gt;. &lt;em&gt;bipolare&lt;/em&gt; complex. Phylogenetic analyses based on &lt;em&gt;TUB&lt;/em&gt; sequence revealed 11 distinct species within the &lt;em&gt;Lo. bipolare&lt;/em&gt; complex. Morphological features of the ascospores and the anatomical structure of the ascomata from both field collections as well as axenic culture, which have been reported previously as variable features at intraspecific levels, were compared to evaluate the taxonomic reliability of these features. To clarify the generic position of the 11 species, phylogenetic analyses were done on SSU-ITS-LSU-&lt;em&gt;tef1&lt;/em&gt;-&lt;em&gt;rpb2&lt;/em&gt; gene sequences. The &lt;em&gt;Lo&lt;/em&gt;. &lt;em&gt;bipolare&lt;/em&gt; complex shared phylogenetic relationships with &lt;em&gt;Pseudolophiostoma&lt;/em&gt; and &lt;em&gt;Vaginatispora&lt;/em&gt;, and formed an additional five distinct clades from other members of &lt;em&gt;Lophiostomataceae&lt;/em&gt;. According to its phylogenetic position, &lt;em&gt;Lo. bipolare sensu stricto&lt;/em&gt; was distantly related to &lt;em&gt;Lophiostoma&lt;/em&gt; s. str., and formed an independent clade within &lt;em&gt;Lophiostomataceae. Lophiostoma bipolare&lt;/em&gt; s. str. could be distinguished from the other lophiostomataceous genera by the clypeus around the ostiolar neck and by the thin and uniformly thick peridium. A novel genus described as &lt;em&gt;Lentistoma&lt;/em&gt; was established to accommodate this species, and the epitypification of &lt;em&gt;Lentistoma bipolare&lt;/em&gt; (basionym: &lt;em&gt;Massarina bipolaris&lt;/em&gt;) was proposed. Other lineages of the &lt;em&gt;Lo. bipolare&lt;/em&gt; complex could not be separated on the basis of the ascospore size and sheath variations, but were distinguished based on ascomatal features, such as the existence of the clypeus, brown hyphae surrounding the peridium, and the contexture of the peridium, which were stable indicators of generic boundaries in &lt;em&gt;Lophiostomataceae&lt;/em&gt;. Four additional new genera with five new species were recognised based on these morphological differences: &lt;em&gt;Crassiclypeus&lt;/em&gt; (&lt;em&gt;C&lt;/em&gt;. &lt;em&gt;aquaticus&lt;/em&gt;), &lt;em&gt;Flabellascoma&lt;/em&gt; (&lt;em&gt;F&lt;/em&gt;. &lt;em&gt;cycadicola&lt;/em&gt; and &lt;em&gt;F&lt;/em&gt;. &lt;em&gt;minimum&lt;/em&gt;), &lt;em&gt;Leptoparies&lt;/em&gt; (&lt;em&gt;Lep&lt;/em&gt;. &lt;em&gt;palmarum&lt;/em&gt;), and &lt;em&gt;Pseudopaucispora&lt;/em&gt; (&lt;em&gt;Pseudop&lt;/em&gt;. &lt;em&gt;brunneospora&lt;/em&gt;). Three new species were added to &lt;em&gt;Pseudolophiostoma&lt;/em&gt; (&lt;em&gt;Pseudol&lt;/em&gt;. &lt;em&gt;cornisporum&lt;/em&gt;, &lt;em&gt;Pseudol&lt;/em&gt;. &lt;em&gt;obtusisporum&lt;/em&gt;, and &lt;em&gt;Pseudol&lt;/em&gt;. &lt;em&gt;tropicum&lt;/em&gt;) and two new species were added to &lt;em&gt;Vaginatispora&lt;/em&gt; (&lt;em&gt;V&lt;/em&gt;. &lt;em&gt;amygdali&lt;/em&gt; and &lt;em&gt;V&lt;/em&gt;. &lt;em&gt;scabrispora&lt;/em&gt;). The re-evaluation of the validity of several previously recognised genera resulted in the introduction of two new genera with new combinations for &lt;","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"90 ","pages":"Pages 161-189"},"PeriodicalIF":16.5,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.03.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35989670","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 preliminary account of the Cucurbitariaceae","authors":"W.M. Jaklitsch ,&nbsp;J. Checa ,&nbsp;M.N. Blanco ,&nbsp;I. Olariaga ,&nbsp;S. Tello ,&nbsp;H. Voglmayr","doi":"10.1016/j.simyco.2017.11.002","DOIUrl":"10.1016/j.simyco.2017.11.002","url":null,"abstract":"<div><p>Fresh collections, type studies and molecular phylogenetic analyses of a multigene matrix of partial nuSSU-ITS-LSU rDNA, <em>rpb2</em>, <em>tef1</em> and <em>tub2</em> sequences were used to evaluate the boundaries of <em>Cucurbitaria</em> in a strict sense and of several related genera of the <em>Cucurbitariaceae</em>. Two species are recognised in <em>Cucurbitaria</em> and 19 in <em>Neocucurbitaria</em>. The monotypic genera <em>Astragalicola</em>, <em>Cucitella</em>, <em>Parafenestella</em>, <em>Protofenestella</em>, and <em>Seltsamia</em> are described as new. <em>Fenestella</em> is here included as its generic type <em>F. fenestrata</em> (= <em>F. princeps</em>), which is lecto- and epitypified. <em>Fenestella mackenzei</em> and <em>F. ostryae</em> are combined in <em>Parafenestella</em>. Asexual morphs of <em>Cucurbitariaceae</em>, where known, are all pyrenochaeta- or phoma-like. Comparison of the phylogenetic analyses of the ITS-LSU and combined matrices demonstrate that at least <em>rpb2</em> sequences should be added whenever possible to improve phylogenetic resolution of the tree backbone; in addition, the <em>tef1</em> introns should be added as well to improve delimitation of closely related species.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"90 ","pages":"Pages 71-118"},"PeriodicalIF":16.5,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2017.11.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35687356","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":"Temporal variation of fungal diversity in a mosaic landscape in Germany","authors":"S. Rudolph ,&nbsp;J.G. Maciá-Vicente ,&nbsp;H. Lotz-Winter ,&nbsp;M. Schleuning ,&nbsp;M. Piepenbring","doi":"10.1016/j.simyco.2018.01.001","DOIUrl":"10.1016/j.simyco.2018.01.001","url":null,"abstract":"<div><p>This study aims at characterizing the diversity and temporal changes of species richness and composition of fungi in an ecotone of a forest border and a meadow in the Taunus mountain range in Germany. All macroscopically visible, epigeous fungi and vascular plants were sampled monthly over three years, together with climatic variables like humidity and temperature that influence fungal diversity and composition as shown by previous studies. In this mosaic landscape, a total of 855 fungal species were collected and identified based on morphological features, the majority of which belonged to <em>Ascomycota</em> (51 %) and <em>Basidiomycota</em> (45 %). Records of fungal species and plant species (218) for this area yielded a fungus to plant species ratio of 4:1, with a plant species accumulation curve that reached saturation. The three years of monitoring, however, were not sufficient to reveal the total fungal species richness and estimation factors showed that a fungus to plant species ratio of 6:1 may be reached by further sampling efforts. The effect of climatic conditions on fungal species richness differed depending on the taxonomic and ecological group, with temporal patterns of occurrence of <em>Basidiomycota</em> and mycorrhizal fungi being strongly associated with temperature and humidity, whereas the other fungal groups were only weakly related to abiotic conditions. In conclusion, long-term, monthly surveys over several years yield a higher diversity of macroscopically visible fungi than standard samplings of fungi in autumn. The association of environmental variables with the occurrence of specific fungal guilds may help to improve estimators of fungal richness in temperate regions.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"89 ","pages":"Pages 95-104"},"PeriodicalIF":16.5,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.01.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36229933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. violaceum","authors":"P. Zhan ,&nbsp;K. Dukik ,&nbsp;D. Li ,&nbsp;J. Sun ,&nbsp;J.B. Stielow ,&nbsp;B. Gerrits van den Ende ,&nbsp;B. Brankovics ,&nbsp;S.B.J. Menken ,&nbsp;H. Mei ,&nbsp;W. Bao ,&nbsp;G. Lv ,&nbsp;W. Liu ,&nbsp;G.S. de Hoog","doi":"10.1016/j.simyco.2018.02.004","DOIUrl":"10.1016/j.simyco.2018.02.004","url":null,"abstract":"<div><p><em>Trichophyton rubrum</em> and <em>T. violaceum</em> are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the <em>T. rubrum</em> complex with analysis of rDNA ITS supplemented with LSU, <em>TUB2, TEF3</em> and ribosomal protein L10 gene sequences. In order to explore genomic differences between <em>T. rubrum</em> and <em>T. violaceum</em>, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of <em>Arthroderma</em>, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus <em>Trichophyton</em>. Significant genome conservation between <em>T. rubrum</em> and <em>T. violaceum</em> was observed, with a high similarity at the nucleic acid level of 99.38 % identity. <em>Trichophyton violaceum</em> contains more paralogs than <em>T. rubrum</em>. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between <em>T. rubrum</em> and <em>T. violaceum</em>, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of <em>T. rubrum</em> and <em>T. violaceum</em> underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"89 ","pages":"Pages 153-175"},"PeriodicalIF":16.5,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2018.02.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36229938","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}