Studies in Mycology最新文献

{"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}

{"title":"Fusarium: more than a node or a foot-shaped basal cell","authors":"P.W. Crous ,&nbsp;L. Lombard ,&nbsp;M. Sandoval-Denis ,&nbsp;K.A. Seifert ,&nbsp;H.-J. Schroers ,&nbsp;P. Chaverri ,&nbsp;J. Gené ,&nbsp;J. Guarro ,&nbsp;Y. Hirooka ,&nbsp;K. Bensch ,&nbsp;G.H.J. Kema ,&nbsp;S.C. Lamprecht ,&nbsp;L. Cai ,&nbsp;A.Y. Rossman ,&nbsp;M. Stadler ,&nbsp;R.C. Summerbell ,&nbsp;J.W. Taylor ,&nbsp;S. Ploch ,&nbsp;C.M. Visagie ,&nbsp;N. Yilmaz ,&nbsp;M. Thines","doi":"10.1016/j.simyco.2021.100116","DOIUrl":"https://doi.org/10.1016/j.simyco.2021.100116","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family &lt;em&gt;Nectriaceae&lt;/em&gt;. Thus, an alternate hypothesis, namely a very broad concept of the genus &lt;em&gt;Fusarium&lt;/em&gt; was proposed. In doing so, however, a significant body of data that supports distinct genera in &lt;em&gt;Nectriaceae&lt;/em&gt; based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of &lt;em&gt;Fusarium&lt;/em&gt; at the F1 node in &lt;em&gt;Nectriaceae&lt;/em&gt;. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents &lt;em&gt;Fusarium sensu stricto&lt;/em&gt; as defined by &lt;em&gt;F. sambucinum&lt;/em&gt; (sexual morph synonym &lt;em&gt;Gibberella pulicaris&lt;/em&gt;). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of &lt;em&gt;Fusarium.&lt;/em&gt; Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various &lt;em&gt;Nectriaceae&lt;/em&gt; lineages proposed as members of &lt;em&gt;Fusarium&lt;/em&gt;. Species of &lt;em&gt;Fusarium s. str.&lt;/em&gt; are characterised by &lt;em&gt;Gibberella&lt;/em&gt; sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of &lt;em&gt;Fusarium&lt;/em&gt; presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout &lt;em&gt;Nectriaceae&lt;/em&gt;. Thus, the very broad circumscription of &lt;em&gt;Fusarium&lt;/em&gt; is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout &lt;em&gt;Nectriaceae&lt;/em&gt; (&lt;em&gt;e.g.&lt;/em&gt;, &lt;em&gt;Cosmosporella&lt;/em&gt;, &lt;em&gt;Macroconia&lt;/em&gt;, &lt;em&gt;Microcera&lt;/em&gt;). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of &lt;em&gt;Fusarium&lt;/em&gt;. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at &lt;span&gt;www.fusarium.org&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (&lt;em&gt;act1&lt;/em&gt;, &lt;em&gt;CaM&lt;/em&gt;, &lt;em&gt;his3&lt;/em&gt;, &lt;em&gt;rpb1&lt;/em&gt;, &lt;em&gt;rpb2&lt;/em&gt;, &lt;em&gt;tef1&lt;/em&gt;, &lt;em&gt;tub2&lt;/em&gt;, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in &lt;em&gt;Fusarium&lt;/em&gt; up to January 2021 as","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"98 ","pages":"Article 100116"},"PeriodicalIF":16.5,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2021.100116","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92115557","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 global epidemiology of emerging Histoplasma species in recent years","authors":"A.M. Rodrigues ,&nbsp;M.A. Beale ,&nbsp;F. Hagen ,&nbsp;M.C. Fisher ,&nbsp;P.P.D. Terra ,&nbsp;S. de Hoog ,&nbsp;R.S.N. Brilhante ,&nbsp;R. de Aguiar Cordeiro ,&nbsp;D. de Souza Collares Maia Castelo-Branco ,&nbsp;M.F.G. Rocha ,&nbsp;J.J.C. Sidrim ,&nbsp;Z.P. de Camargo","doi":"10.1016/j.simyco.2020.02.001","DOIUrl":"10.1016/j.simyco.2020.02.001","url":null,"abstract":"<div><p>Histoplasmosis is a serious infectious disease in humans caused by <em>Histoplasma</em> spp. (Onygenales), whose natural reservoirs are thought to be soil enriched with bird and bat guano. The true global burden of histoplasmosis is underestimated and frequently the pulmonary manifestations are misdiagnosed as tuberculosis. Molecular data on epidemiology of <em>Histoplasma</em> are still scarce, even though there is increasing recognition of histoplasmosis in recent years in areas distant from the traditional endemic regions in the Americas. We used multi-locus sequence data from protein coding loci (ADP-ribosylation factor, H antigen precursor, and delta-9 fatty acid desaturase), DNA barcoding (ITS1/2+5.8s), AFLP markers and mating type analysis to determine the genetic diversity, population structure and recognise the existence of different phylogenetic species among 436 isolates of <em>Histoplasma</em> obtained globally. Our study describes new phylogenetic species and the molecular characteristics of <em>Histoplasma</em> lineages causing outbreaks with a high number of severe outcomes in Northeast Brazil between 2011 and 2015. Genetic diversity levels provide evidence for recombination, common ancestry and clustering of Brazilian isolates at different geographic scales with the emergence of LAm C, a new genotype assigned to a separate population cluster in Northeast Brazil that exhibited low diversity indicative of isolation. The global survey revealed that the high genetic variability among Brazilian isolates along with the presence of divergent cryptic species and/or genotypes may support the hypothesis of Brazil being the center of dispersion of <em>Histoplasma</em> in South America, possibly with the contribution of migratory hosts such as birds and bats. Outside Brazil, the predominant species depends on the region. We confirm that histoplasmosis has significantly broadened its area of occurrence, an important feature of emerging pathogens. From a practical point of view, our data point to the emergence of histoplasmosis caused by a plethora of genotypes, and will enable epidemiological analysis focused on understanding the processes that lead to histoplasmosis. Further, the description of this diversity opens avenues for comparative genomic studies, which will allow progress toward a consensus taxonomy, improve understanding of the presence of hybrids in natural populations of medically relevant fungi, test reproductive barriers and to explore the significance of this variation.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"97 ","pages":"Article 100095"},"PeriodicalIF":16.5,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2020.02.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38724746","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":"Reconsideration of species boundaries and proposed DNA barcodes for Calonectria","authors":"Q.L. Liu ,&nbsp;J.Q. Li ,&nbsp;M.J. Wingfield ,&nbsp;T.A. Duong ,&nbsp;B.D. Wingfield ,&nbsp;P.W. Crous ,&nbsp;S.F. Chen","doi":"10.1016/j.simyco.2020.08.001","DOIUrl":"10.1016/j.simyco.2020.08.001","url":null,"abstract":"<div><p><em>Calonectria</em> represents a genus of phytopathogenic ascomycetous fungi with a worldwide distribution. In recent years, there has been an increase in the number of taxonomic studies on these fungi. Currently, there are 169 described species of <em>Calonectria</em> based on comparisons of DNA sequence data, combined with morphological characteristics. However, for some of these species, the sequence data utilised at the time of their description were relatively limited. This has justified an urgent need to reconsider the species boundaries for <em>Calonectria</em> based on robust genus-wide phylogenetic analyses. In this study, we utilised 240 available isolates including the ex-types of 128 <em>Calonectria</em> species, and re-sequenced eight gene regions (<em>act</em>, <em>cmdA</em>, <em>his3</em>, ITS, LSU, <em>rpb2, tef1</em> and <em>tub2</em>) for them. Sequences for 44 <em>Calonectria</em> species, for which cultures could not be obtained, were downloaded from GenBank. DNA sequence data of all the 169 <em>Calonectria</em> species were then used to determine their phylogenetic relationships. As a consequence, 51 species were reduced to synonymy, two new species were identified, and the name <em>Ca. lauri</em> was validated. This resulted in the acceptance of 120 clearly defined <em>Calonectria</em> spp. The overall data revealed that the genus includes 11 species complexes, distributed across the Prolate and Sphaero-Naviculate Groups known to divide <em>Calonectria</em>. The results also made it possible to develop a robust set of DNA barcodes for <em>Calonectria</em> spp. To accomplish this goal, we evaluated the outcomes of each of the eight candidate DNA barcodes for the genus, as well as for each of the 11 species complexes. No single gene region provided a clear identity for all <em>Calonectria</em> species. Sequences of the <em>tef1</em> and <em>tub2</em> genes were the most reliable markers; those for the <em>cmdA</em>, <em>his3</em>, <em>rpb2</em> and <em>act</em> gene regions also provided a relatively effective resolution for <em>Calonectria</em> spp., while the ITS and LSU failed to produce useful barcodes for species discrimination. At the species complex level, results showed that the most informative barcodes were inconsistent, but that a combination of six candidate barcodes (<em>tef1</em>, <em>tub2</em>, <em>cmdA</em>, <em>his3</em>, <em>rpb2</em> and <em>act</em>) provided stable and reliable resolution for all 11 species complexes. A six-gene combined phylogeny resolved all 120 <em>Calonectria</em> species, and revealed that <em>tef1</em>, <em>tub2</em>, <em>cmdA</em>, <em>his3</em>, <em>rpb2</em> and <em>act</em> gene regions are effective DNA barcodes for <em>Calonectria</em>.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"97 ","pages":"Article 100106"},"PeriodicalIF":16.5,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2020.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39254345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species","authors":"A.-H. Li ,&nbsp;F.-X. Yuan ,&nbsp;M. Groenewald ,&nbsp;K. Bensch ,&nbsp;A.M. Yurkov ,&nbsp;K. Li ,&nbsp;P.-J. Han ,&nbsp;L.-D. Guo ,&nbsp;M.C. Aime ,&nbsp;J.P. Sampaio ,&nbsp;S. Jindamorakot ,&nbsp;B. Turchetti ,&nbsp;J. Inacio ,&nbsp;B. Fungsin ,&nbsp;Q.-M. Wang ,&nbsp;F.-Y. Bai","doi":"10.1016/j.simyco.2020.01.002","DOIUrl":"10.1016/j.simyco.2020.01.002","url":null,"abstract":"<div><p>Nearly 500 basidiomycetous yeast species were accepted in the latest edition of <em>The Yeasts: A Taxonomic Study</em> published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the <em>Tremellomycetes</em> (<em>Agaricomycotina</em>). The other 61 are distributed in 26 genera in the <em>Pucciniomycotina</em>. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"96 ","pages":"Pages 17-140"},"PeriodicalIF":16.5,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2020.01.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37766339","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":"Identification of Rosellinia species as producers of cyclodepsipeptide PF1022 A and resurrection of the genus Dematophora as inferred from polythetic taxonomy","authors":"K. Wittstein ,&nbsp;A. Cordsmeier ,&nbsp;C. Lambert ,&nbsp;L. Wendt ,&nbsp;E.B. Sir ,&nbsp;J. Weber ,&nbsp;N. Wurzler ,&nbsp;L.E. Petrini ,&nbsp;M. Stadler","doi":"10.1016/j.simyco.2020.01.001","DOIUrl":"10.1016/j.simyco.2020.01.001","url":null,"abstract":"<div><p><em>Rosellinia</em> (<em>Xylariaceae</em>) is a large, cosmopolitan genus comprising over 130 species that have been defined based mainly on the morphology of their sexual morphs. The genus comprises both lignicolous and saprotrophic species that are frequently isolated as endophytes from healthy host plants, and important plant pathogens. In order to evaluate the utility of molecular phylogeny and secondary metabolite profiling to achieve a better basis for their classification, a set of strains was selected for a multi-locus phylogeny inferred from a combination of the sequences of the internal transcribed spacer region (ITS), the large subunit (LSU) of the nuclear rDNA, beta-tubulin (<em>TUB2</em>) and the second largest subunit of the RNA polymerase II (<em>RPB2</em>). Concurrently, various strains were surveyed for production of secondary metabolites. Metabolite profiling relied on methods with high performance liquid chromatography with diode array and mass spectrometric detection (HPLC-DAD/MS) as well as preparative isolation of the major components after re-fermentation followed by structure elucidation using nuclear magnetic resonance (NMR) spectroscopy and high resolution mass spectrometry (HR-MS). Two new and nine known isopimarane diterpenoids were identified during our mycochemical studies of two selected <em>Dematophora</em> strains and the metabolites were tested for biological activity. In addition, the nematicidal cyclodepsipeptide PF1022 A was purified and identified from a culture of <em>Rosellinia corticium,</em> which is the first time that this endophyte-derived drug precursor has been identified unambiguously from an ascospore-derived isolate of a <em>Rosellinia</em> species. While the results of this first HPLC profiling were largely inconclusive regarding the utility of secondary metabolites as genus-specific chemotaxonomic markers, the phylogeny clearly showed that species featuring a dematophora-like asexual morph were included in a well-defined clade, for which the genus <em>Dematophora</em> is resurrected. <em>Dematophora</em> now comprises all previously known important plant pathogens in the genus such as <em>D. arcuata</em>, <em>D. bunodes</em>, <em>D. necatrix</em> and <em>D. pepo</em>, while <em>Rosellinia s. str</em>. comprises those species that are known to have a geniculosporium-like or nodulisporium-like asexual morph, or where the asexual morph remains unknown. The extensive morphological studies of L.E. Petrini served as a basis to transfer several further species from <em>Rosellinia</em> to <em>Dematophora</em>, based on the morphology of their asexual morphs. However, most species of <em>Rosellinia</em> and allies still need to be recollected in fresh state, cultured, and studied for their morphology and their phylogenetic affinities before the infrageneric relationships can be clarified.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"96 ","pages":"Pages 1-16"},"PeriodicalIF":16.5,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2020.01.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37733030","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 phoma-like dilemma","authors":"L.W. Hou ,&nbsp;J.Z. Groenewald ,&nbsp;L.H. Pfenning ,&nbsp;O. Yarden ,&nbsp;P.W. Crous ,&nbsp;L. Cai","doi":"10.1016/j.simyco.2020.05.001","DOIUrl":"10.1016/j.simyco.2020.05.001","url":null,"abstract":"<div><p>Species of <em>Didymellaceae</em> have a cosmopolitan distribution and are geographically widespread, occurring in diverse ecosystems. The family includes several important plant pathogenic fungi associated with fruit, leaf, stem and root diseases on a wide variety of hosts, as well as endophytic, saprobic and clinically relevant species. The <em>Didymellaceae</em> was recently revised based on morphological and phylogenetic analyses of ex-type strains subjected to DNA sequencing of partial gene data of the LSU, ITS, <em>rpb2</em> and <em>tub2</em> loci. Several poly- and paraphyletic genera, including <em>Ascochyta</em>, <em>Didymella</em> and <em>Phoma</em> were redefined, along with the introduction of new genera. In the present study, a global collection of 1 124 <em>Didymellaceae</em> strains from 92 countries, 121 plant families and 55 other substrates, including air, coral, human tissues, house dust, fungi, insects, soil, and water were examined via multi-locus phylogenetic analyses and detailed morphological comparisons, representing the broadest sampling of <em>Didymellaceae</em> to date. Among these, 97 isolates representing seven new genera, 40 new species and 21 new combinations were newly introduced in <em>Didymellaceae</em>. In addition, six epitypes and six neotypes were designated to stabilise the taxonomy and use of older names. A robust, multi-locus reference phylogenetic tree of <em>Didymellaceae</em> was generated. In addition, <em>rpb2</em> was revealed as the most effective locus for the identification of <em>Didymellaceae</em> at species level, and is proposed as a secondary DNA marker for the family.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"96 ","pages":"Pages 309-396"},"PeriodicalIF":16.5,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2020.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38455759","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":"Venturiales","authors":"M. Shen ,&nbsp;J.Q. Zhang ,&nbsp;L.L. Zhao ,&nbsp;J.Z. Groenewald ,&nbsp;P.W. Crous ,&nbsp;Y. Zhang","doi":"10.1016/j.simyco.2020.03.001","DOIUrl":"10.1016/j.simyco.2020.03.001","url":null,"abstract":"<div><p>Members of <em>Venturiales</em> (<em>Dothideomycetes</em>) are widely distributed, and comprise saprobes, as well as plant, human and animal pathogens. In spite of their economic importance, the general lack of cultures and DNA data has resulted in taxa being poorly resolved. In the present study five loci, ITS, LSU rDNA, <em>tef1</em>, <em>tub2</em> and <em>rpb2</em> are used for analysing 115 venturialean taxa representing 30 genera in three families in the current classification of <em>Venturiales</em>. Based on the multigene phylogenetic analysis, morphological and ecological characteristics, one new family, <em>Cylindrosympodiaceae</em>, and eight new genera are described, namely <em>Bellamyces</em>, <em>Fagicola, Fraxinicola</em>, <em>Fuscohilum,</em> <em>Neofusicladium</em>, <em>Parafusicladium</em>, <em>Pinaceicola</em> and <em>Sterila</em>. In addition, 12 species are described as new to science, and 41 new combinations are proposed. The taxonomic status of 153 species have been re-evaluated with 20 species excluded from <em>Venturiales</em>. Based on this revision of <em>Venturiales</em>, morphological characteristics such as conidial arrangement (solitary or in chains) or conidiogenesis (blastic-solitary, sympodial or annellidic), proved to be significant at generic level. <em>Venturia</em> as currently defined represents a generic complex. Furthermore, plant pathogens appear more terminal in phylogenetic analyses within <em>Venturiaceae</em> and <em>Sympoventuriaceae</em>, suggesting that the ancestral state of <em>Venturiales</em> is most likely saprobic.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"96 ","pages":"Pages 185-308"},"PeriodicalIF":16.5,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2020.03.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38360312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic origins and family classification of typhuloid fungi, with emphasis on Ceratellopsis, Macrotyphula and Typhula (Basidiomycota)","authors":"I. Olariaga ,&nbsp;S. Huhtinen ,&nbsp;T. Læssøe ,&nbsp;J.H. Petersen ,&nbsp;K. Hansen","doi":"10.1016/j.simyco.2020.05.003","DOIUrl":"10.1016/j.simyco.2020.05.003","url":null,"abstract":"<div><p>Typhuloid fungi are a very poorly known group of tiny clavarioid homobasidiomycetes. The phylogenetic position and family classification of the genera targeted here, <em>Ceratellopsis</em>, <em>Macrotyphula</em>, <em>Pterula sensu lato</em> and <em>Typhula</em>, are controversial and based on unresolved phylogenies. Our six-gene phylogeny with an expanded taxon sampling shows that typhuloid fungi evolved at least twice in the <em>Agaricales</em> (<em>Pleurotineae</em>, <em>Clavariineae</em>) and once in the <em>Hymenochaetales</em>. <em>Macrotyphula</em>, <em>Pterulicium</em> and <em>Typhula</em> are nested within the <em>Pleurotineae</em>. The type of <em>Typhula</em> (1818) and <em>Sclerotium</em> (1790), <em>T. phacorrhiza</em> and <em>S. complanatum</em> (synonym <em>T. phacorrhiza</em>), are encompassed in the <em>Macrotyphula</em> clade that is distantly related to a monophyletic group formed by species usually assigned to <em>Typhula</em>. Thus, the correct name for <em>Macrotyphula</em> (1972) and <em>Typhula</em> is <em>Sclerotium</em> and all <em>Typhula</em> species but those in the <em>T. phacorrhiza</em> group need to be transferred to <em>Pistillaria</em> (1821). To avoid undesirable nomenclatural changes, we suggest to conserve <em>Typhula</em> with <em>T. incarnata</em> as type. <em>Clavariaceae</em> is supported as a separate, early diverging lineage within <em>Agaricales</em>, with <em>Hygrophoraceae</em> as a successive sister taxon to the rest of the <em>Agaricales</em>. <em>Ceratellopsis s. auct.</em> is polyphyletic because <em>C. acuminata</em> nests in <em>Clavariaceae</em> and <em>C. sagittiformis</em> in the <em>Hymenochaetales</em>. <em>Ceratellopsis</em> is found to be an earlier name for <em>Pterulicium</em>, because the type, <em>C. queletii</em>, represents <em>Pterulicium gracile</em> (synonym <em>Pterula gracilis</em>), deeply nested in the <em>Pterulicium</em> clade. To avoid re-combining a large number of names in <em>Ceratellopsis</em> we suggest to conserve it with <em>C. acuminata</em> as type. The new genus <em>Bryopistillaria</em> is created to include <em>C. sagittiformis</em>. The families <em>Sarcomyxaceae</em> and <em>Phyllotopsidaceae</em>, and the suborder <em>Clavariineae</em>, are described as new. Six new combinations are proposed and 15 names typified.</p></div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"96 ","pages":"Pages 155-184"},"PeriodicalIF":16.5,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2020.05.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38255777","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}