Studies in Mycology最新文献

{"title":"A monograph of <i>Aspergillus</i> section <i>Candidi</i>.","authors":"K Glässnerová,&nbsp;F Sklenář,&nbsp;Ž Jurjević,&nbsp;J Houbraken,&nbsp;T Yaguchi,&nbsp;C M Visagie,&nbsp;J Gené,&nbsp;J P Z Siqueira,&nbsp;A Kubátová,&nbsp;M Kolařík,&nbsp;V Hubka","doi":"10.3114/sim.2022.102.01","DOIUrl":"https://doi.org/10.3114/sim.2022.102.01","url":null,"abstract":"<p><p><i>Aspergillus</i> section <i>Candidi</i> encompasses white- or yellow-sporulating species mostly isolated from indoor and cave environments, food, feed, clinical material, soil and dung. Their identification is non-trivial due to largely uniform morphology. This study aims to re-evaluate the species boundaries in the section <i>Candidi</i> and present an overview of all existing species along with information on their ecology. For the analyses, we assembled a set of 113 strains with diverse origin. For the molecular analyses, we used DNA sequences of three house-keeping genes (<i>benA</i>, <i>CaM</i> and <i>RPB2</i>) and employed species delimitation methods based on a multispecies coalescent model. Classical phylogenetic methods and genealogical concordance phylogenetic species recognition (GCPSR) approaches were used for comparison. Phenotypic studies involved comparisons of macromorphology on four cultivation media, seven micromorphological characters and growth at temperatures ranging from 10 to 45 °C. Based on the integrative approach comprising four criteria (phylogenetic and phenotypic), all currently accepted species gained support, while two new species are proposed (<i>A. magnus</i> and <i>A. tenebricus</i>). In addition, we proposed the new name <i>A. neotritici</i> to replace an invalidly described <i>A. tritici</i>. The revised section <i>Candidi</i> now encompasses nine species, some of which manifest a high level of intraspecific genetic and/or phenotypic variability (<i>e.g.</i>, <i>A. subalbidus</i> and <i>A. campestris</i>) while others are more uniform (<i>e.g.</i>, <i>A. candidus</i> or <i>A. pragensis</i>). The growth rates on different media and at different temperatures, colony colours, production of soluble pigments, stipe dimensions and vesicle diameters contributed the most to the phenotypic species differentiation. <b>Taxonomic novelties: New species:</b> <i>Aspergillus magnus</i> Glässnerová & Hubka; <i>Aspergillus neotritici</i> Glässnerová & Hubka; <i>Aspergillus tenebricus</i> Houbraken, Glässnerová & Hubka. <b>Citation:</b> Glässnerová K, Sklenář F, Jurjević Ž, Houbraken J, Yaguchi T, Visagie CM, Gené J, Siqueira JPZ, Kubátová A, Kolařík M, Hubka V (2022). A monograph of <i>Aspergillus</i> section <i>Candidi</i>. <i>Studies in Mycology</i> <b>102</b>: 1-51. doi: 10.3114/sim.2022.102.01.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"102 ","pages":"1-51"},"PeriodicalIF":16.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10330037","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":"Reducing the number of accepted species in <i>Aspergillus</i> series <i>Nigri</i>.","authors":"C Bian, Y Kusuya, F Sklenář, E D'hooge, T Yaguchi, S Ban, C M Visagie, J Houbraken, H Takahashi, V Hubka","doi":"10.3114/sim.2022.102.03","DOIUrl":"10.3114/sim.2022.102.03","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The &lt;i&gt;Aspergillus&lt;/i&gt; series &lt;i&gt;Nigri&lt;/i&gt; contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (&lt;i&gt;benA&lt;/i&gt;, &lt;i&gt;CaM&lt;/i&gt; and &lt;i&gt;RPB2&lt;/i&gt;) for 276 strains from series &lt;i&gt;Nigri&lt;/i&gt; and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: &lt;i&gt;A. niger&lt;/i&gt;, &lt;i&gt;A. tubingensis&lt;/i&gt; and &lt;i&gt;A. brasiliensis&lt;/i&gt;. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on &lt;i&gt;benA&lt;/i&gt;, &lt;i&gt;CaM&lt;/i&gt; and &lt;i&gt;RPB2&lt;/i&gt; is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the &lt;i&gt;A. niger&lt;/i&gt; and &lt;i&gt;A. brasiliensis&lt;/i&gt; lineages, while one to four species were inconsistently delimited in the &lt;i&gt;A. tubingensis&lt;/i&gt; lineage. After considering all of these results and their practical implications, we propose that the revised series &lt;i&gt;Nigri&lt;/i&gt; includes six species: &lt;i&gt;A. brasiliensis&lt;/i&gt;, &lt;i&gt;A. eucalypticola&lt;/i&gt;, &lt;i&gt;A. luchuensis&lt;/i&gt; (syn&lt;i&gt;. A. piperis&lt;/i&gt;), &lt;i&gt;A. niger&lt;/i&gt; (syn. &lt;i&gt;A. vinaceus&lt;/i&gt; and &lt;i&gt;A. welwitschiae&lt;/i&gt;), &lt;i&gt;A. tubingensis&lt;/i&gt; (syn. &lt;i&gt;A. chiangmaiensis&lt;/i&gt;, &lt;i&gt;A. costaricensis&lt;/i&gt;, &lt;i&gt;A. neoniger&lt;/i&gt; and &lt;i&gt;A. pseudopiperis&lt;/i&gt;) and &lt;i&gt;A. vadensis&lt;/i&gt;. We also showed that the intraspecific genetic variability in the redefined &lt;i&gt;A. niger&lt;/i&gt; and &lt;i&gt;A. tubingensis&lt;/i&gt; does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy. &lt;b&gt;Cita","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"102 ","pages":"95-132"},"PeriodicalIF":14.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9240643","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":"Fungal communities in soils under global change.","authors":"P Baldrian,&nbsp;L Bell-Dereske,&nbsp;C Lepinay,&nbsp;T Větrovský,&nbsp;P Kohout","doi":"10.3114/sim.2022.103.01","DOIUrl":"https://doi.org/10.3114/sim.2022.103.01","url":null,"abstract":"<p><p>Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO₂ concentration, temperature, change of precipitation and nitrogen (N) deposition, affect fungal species and communities in soils. Although the observed effects depend on the size and duration of change and reflect local conditions, increased N deposition seems to have the most profound effect on fungal communities. The plant-mutualistic fungal guilds - ectomycorrhizal fungi and arbuscular mycorrhizal fungi - appear to be especially responsive to global change factors with N deposition and warming seemingly having the strongest adverse effects. While global change effects on fungal biodiversity seem to be limited, multiple studies demonstrate increases in abundance and dispersal of plant pathogenic fungi. Additionally, ecosystems weakened by global change-induced phenomena, such as drought, are more vulnerable to pathogen outbreaks. The shift from mutualistic fungi to plant pathogens is likely the largest potential threat for the future functioning of natural and managed ecosystems. However, our ability to predict global change effects on fungi is still insufficient and requires further experimental work and long-term observations. <b>Citation:</b> Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. <i>Studies in Mycology</i> <b>103</b>: 1-24. doi: 10.3114/sim.2022.103.01.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"103 ","pages":"1-24"},"PeriodicalIF":16.5,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9886077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10678821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Mortierellaceae</i> from subalpine and alpine habitats: new species of <i>Entomortierella, Linnemannia, Mortierella, Podila</i> and <i>Tyroliella gen. nov.</i>","authors":"A Telagathoti, M Probst, E Mandolini, U Peintner","doi":"10.3114/sim.2022.103.02","DOIUrl":"10.3114/sim.2022.103.02","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Fungi are incredibly diverse, but they are unexplored, especially in the subalpine and alpine zone. &lt;i&gt;Mortierellaceae&lt;/i&gt; are certainly one of the most abundant, species-rich, and widely distributed cultivable soil fungal families in terrestrial habitats, including subalpine and alpine zones. The phylogeny of &lt;i&gt;Mortierellaceae&lt;/i&gt; was recently resolved based on current state of the art molecular techniques, and the paraphyletic genus &lt;i&gt;Mortierella sensu lato&lt;/i&gt; (&lt;i&gt;s.l.&lt;/i&gt;) was divided into 13 monophyletic genera. Our extensive sampling campaigns in the Austrian Alps resulted in 139 different &lt;i&gt;Mortierellaceae&lt;/i&gt; pure culture isolates representing 13 new species. For the definition of taxa, we applied both classical morphological criteria, as well as modern DNA-based methods. Phylogenetic relationships were resolved based on the ribosomal DNA internal transcribed spacer (rDNA ITS), the large subunit (LSU), and the DNA-directed RNA polymerase II largest subunit 1 (&lt;i&gt;RPB1&lt;/i&gt;). In this study, we proposed a new genus and described 13 new species belonging to the genera &lt;i&gt;Entomortierella&lt;/i&gt;, &lt;i&gt;Linnemannia&lt;/i&gt;, &lt;i&gt;Mortierella&lt;/i&gt; and &lt;i&gt;Podila&lt;/i&gt;. In addition, we proposed eight new combinations, re-defined &lt;i&gt;E. jenkinii&lt;/i&gt; at species level, defined a neotype for &lt;i&gt;M. alpina&lt;/i&gt; and lecto- as well as epitypes for &lt;i&gt;M. fatshederae&lt;/i&gt;, &lt;i&gt;M. jenkinii,&lt;/i&gt; and &lt;i&gt;M. longigemmata.&lt;/i&gt; The rDNA ITS region is generally applied as classical barcoding gene for fungi. However, the obtained phylogenetic resolution is often too low for an accurate identification of closely related species of &lt;i&gt;Mortierellaceae&lt;/i&gt;, especially for small sampling sizes. In such cases, unambiguous identification can be obtained based on morphological characters of pure culture isolates. Therefore, we also provide dichotomous keys for species identification within phylogenetic lineages. &lt;b&gt;Taxonomic novelties:&lt;/b&gt; &lt;b&gt;new genus:&lt;/b&gt; &lt;i&gt;Tyroliella&lt;/i&gt; Telagathoti, Probst & Peintner; &lt;b&gt;New species:&lt;/b&gt; &lt;i&gt;Entomortierella galaxiae&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Linnemannia bainierella&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Linnemannia stellaris&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Linnemannia nimbosa&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Linnemannia mannui&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Linnemannia friederikiana&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Linnemannia scordiella&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Linnemannia solitaria&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Mortierella triangularis&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Mortierella lapis&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Podila himami&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Podila occulta&lt;/i&gt; Telagathoti, M. Probst & Peintner, &lt;i&gt;Tyroliella animus-liberi&lt;/i&gt; Telagathoti, Probst & Peintner; &lt;b&gt;New combinations:&lt;/b&gt; &lt;i&gt;Entomortierella basiparvispora&lt;/i&gt; (W. Gams & Grinb.) Telagathoti, M. Probst & Peintner, &lt;i&gt;Entomortierella jenkinii&lt;/i&gt; (A.L. Sm.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"103 ","pages":"25-58"},"PeriodicalIF":14.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10277274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10066992","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 review of <i>Hyphodiscaceae</i>.","authors":"L Quijada,&nbsp;H O Baral,&nbsp;P R Johnston,&nbsp;K Pärtel,&nbsp;J K Mitchell,&nbsp;T Hosoya,&nbsp;H Madrid,&nbsp;T Kosonen,&nbsp;S Helleman,&nbsp;E Rubio,&nbsp;E Stöckli,&nbsp;S Huhtinen,&nbsp;D H Pfister","doi":"10.3114/sim.2022.103.03","DOIUrl":"https://doi.org/10.3114/sim.2022.103.03","url":null,"abstract":"<p><p>In a recently published classification scheme for <i>Leotiomycetes</i>, the new family <i>Hyphodiscaceae</i> was erected; unfortunately, this study was rife with phylogenetic misinterpretations and hampered by a poor understanding of this group of fungi. This manifested in the form of an undiagnostic familial description, an erroneous familial circumscription, and the redescription of the type species of an included genus as a new species in a different genus. The present work corrects these errors by incorporating new molecular data from this group into phylogenetic analyses and examining the morphological features of the included taxa. An emended description of <i>Hyphodiscaceae</i> is provided, notes and descriptions of the included genera are supplied, and keys to genera and species in <i>Hyphodiscaceae</i> are supplied. <i>Microscypha cajaniensis</i> is combined in <i>Hyphodiscus</i>, and <i>Scolecolachnum nigricans</i> is a taxonomic synonym of <i>Fuscolachnum pteridis</i>. Future work in this family should focus on increasing phylogenetic sampling outside of Eurasia and better characterising described species to help resolve outstanding issues. <b>Citation:</b> Quijada L, Baral HO, Johnston PR, Pärtel K, Mitchell JK, Hosoya T, Madrid H, Kosonen T, Helleman S, Rubio E, Stöckli E, Huhtinen S, Pfister DH (2022). A review of <i>Hyphodiscaceae</i>. <i>Studies in Mycology</i> <b>103</b>: 59-85. doi: 10.3114/sim.2022.103.03.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"103 ","pages":"59-85"},"PeriodicalIF":16.5,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10277273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10066988","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":"Consolidation of <i>Chloridium</i>: new classification into eight sections with 37 species and reinstatement of the genera <i>Gongromeriza</i> and <i>Psilobotrys</i>.","authors":"M Réblová,&nbsp;M Hernández-Restrepo,&nbsp;F Sklenář,&nbsp;J Nekvindová,&nbsp;K Réblová,&nbsp;M Kolařík","doi":"10.3114/sim.2022.103.04","DOIUrl":"https://doi.org/10.3114/sim.2022.103.04","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Chloridium&lt;/i&gt; is a little-studied group of soil- and wood-inhabiting dematiaceous hyphomycetes that share a rare mode of phialidic conidiogenesis on multiple loci. The genus has historically been divided into three morphological sections, &lt;i&gt;i.e.&lt;/i&gt; &lt;i&gt;Chloridium&lt;/i&gt;, &lt;i&gt;Gongromeriza&lt;/i&gt;, and &lt;i&gt;Psilobotrys&lt;/i&gt;. Sexual morphs have been placed in the widely perceived genus &lt;i&gt;Chaetosphaeria&lt;/i&gt;, but unlike their asexual counterparts, they show little or no morphological variation. Recent molecular studies have expanded the generic concept to include species defined by a new set of morphological characters, such as the collar-like hyphae, setae, discrete phialides, and penicillately branched conidiophores. The study is based on the consilience of molecular species delimitation methods, phylogenetic analyses, ancestral state reconstruction, morphological hypotheses, and global biogeographic analyses. The multilocus phylogeny demonstrated that the classic concept of &lt;i&gt;Chloridium&lt;/i&gt; is polyphyletic, and the original sections are not congeneric. Therefore, we abolish the existing classification and propose to restore the generic status of &lt;i&gt;Gongromeriza&lt;/i&gt; and &lt;i&gt;Psilobotrys&lt;/i&gt;. We present a new generic concept and define &lt;i&gt;Chloridium&lt;/i&gt; as a monophyletic, polythetic genus comprising 37 species distributed in eight sections. In addition, of the taxa earlier referred to &lt;i&gt;Gongromeriza&lt;/i&gt;, two have been redisposed to the new genus &lt;i&gt;Gongromerizella&lt;/i&gt;. Analysis of published metabarcoding data showed that &lt;i&gt;Chloridium&lt;/i&gt; is a common soil fungus representing a significant (0.3 %) proportion of sequence reads in environmental samples deposited in the GlobalFungi database. The analysis also showed that they are typically associated with forest habitats, and their distribution is strongly influenced by climate, which is confirmed by our data on their ability to grow at different temperatures. We demonstrated that &lt;i&gt;Chloridium&lt;/i&gt; forms species-specific ranges of distribution, which is rarely documented for microscopic soil fungi. Our study shows the feasibility of using the GlobalFungi database to study the biogeography and ecology of fungi. &lt;b&gt;Taxonomic novelties:&lt;/b&gt; &lt;b&gt;New genus:&lt;/b&gt; &lt;i&gt;Gongromerizella&lt;/i&gt; Réblová; &lt;b&gt;New sections:&lt;/b&gt; &lt;i&gt;Chloridium&lt;/i&gt; section &lt;i&gt;Cryptogonytrichum&lt;/i&gt; Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, &lt;i&gt;Chloridium&lt;/i&gt; section &lt;i&gt;Gonytrichopsis&lt;/i&gt; Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, &lt;i&gt;Chloridium&lt;/i&gt; section &lt;i&gt;Metachloridium&lt;/i&gt; Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, &lt;i&gt;Chloridium&lt;/i&gt; section &lt;i&gt;Volubilia&lt;/i&gt; Réblová, Hern.-Restr., M. Kolařík & F. Sklenar; &lt;b&gt;New species:&lt;/b&gt; &lt;i&gt;Chloridium&lt;/i&gt; &lt;i&gt;bellum&lt;/i&gt; Réblová & Hern.-Restr., &lt;i&gt;Chloridium biforme&lt;/i&gt; Réblová & Hern.-Restr., &lt;i&gt;Chloridium detriticola&lt;/i&gt; Réblová & Hern.-Restr., &lt;i&gt;Chloridium&lt;/i&gt; &lt;i&gt;gamsii&lt;/i&gt; Réblová & Hern.-Restr., &lt;i&gt;Chloridium guttiferum&lt;/i&gt; Réblová & Hern.-Restr., &lt;i&gt;Chloridium&lt;/i&gt; &lt;i&gt;moratum&lt;/i&gt; Réblo","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"103 ","pages":"87-212"},"PeriodicalIF":16.5,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10277272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10086095","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":"Genera of phytopathogenic fungi: GOPHY 4.","authors":"Q Chen, M Bakhshi, Y Balci, K D Broders, R Cheewangkoon, S F Chen, X L Fan, D Gramaje, F Halleen, M Horta Jung, N Jiang, T Jung, T Májek, S Marincowitz, I Milenković, L Mostert, C Nakashima, I Nurul Faziha, M Pan, M Raza, B Scanu, C F J Spies, L Suhaizan, H Suzuki, C M Tian, M Tomšovský, J R Úrbez-Torres, W Wang, B D Wingfield, M J Wingfield, Q Yang, X Yang, R Zare, P Zhao, J Z Groenewald, L Cai, P W Crous","doi":"10.3114/sim.2022.101.06","DOIUrl":"10.3114/sim.2022.101.06","url":null,"abstract":"&lt;p&gt;&lt;p&gt;This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including &lt;i&gt;Ascochyta&lt;/i&gt;, &lt;i&gt;Cadophora&lt;/i&gt;, &lt;i&gt;Celoporthe&lt;/i&gt;, &lt;i&gt;Cercospora&lt;/i&gt;, &lt;i&gt;Coleophoma&lt;/i&gt;, &lt;i&gt;Cytospora&lt;/i&gt;, &lt;i&gt;Dendrostoma&lt;/i&gt;, &lt;i&gt;Didymella&lt;/i&gt;, &lt;i&gt;Endothia&lt;/i&gt;, &lt;i&gt;Heterophaeomoniella, Leptosphaerulina&lt;/i&gt;, &lt;i&gt;Melampsora&lt;/i&gt;, &lt;i&gt;Nigrospora&lt;/i&gt;, &lt;i&gt;Pezicula&lt;/i&gt;, &lt;i&gt;Phaeomoniella&lt;/i&gt;, &lt;i&gt;Pseudocercospora&lt;/i&gt;, &lt;i&gt;Pteridopassalora, Zymoseptoria&lt;/i&gt;, and one genus of oomycetes, &lt;i&gt;Phytophthora&lt;/i&gt;. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names. &lt;b&gt;Taxonomic novelties: New genera:&lt;/b&gt; &lt;i&gt;Heterophaeomoniella&lt;/i&gt; L. Mostert, C.F.J. Spies, Halleen & Gramaje, &lt;i&gt;Pteridopassalora&lt;/i&gt; C. Nakash. & Crous; &lt;b&gt;New species:&lt;/b&gt; &lt;i&gt;Ascochyta flava&lt;/i&gt; Qian Chen & L. Cai, &lt;i&gt;Cadophora domestica&lt;/i&gt; L. Mostert, R. van der Merwe, Halleen & Gramaje, &lt;i&gt;Cadophora rotunda&lt;/i&gt; L. Mostert, R. van der Merwe, Halleen & Gramaje, &lt;i&gt;Cadophora vinacea&lt;/i&gt; J.R. Úrbez-Torres, D.T. O'Gorman & Gramaje, &lt;i&gt;Cadophora vivarii&lt;/i&gt; L. Mostert, Havenga, Halleen & Gramaje, &lt;i&gt;Celoporthe foliorum&lt;/i&gt; H. Suzuki, Marinc. & M.J. Wingf., &lt;i&gt;Cercospora alyssopsidis&lt;/i&gt; M. Bakhshi, Zare & Crous, &lt;i&gt;Dendrostoma elaeocarpi&lt;/i&gt; C.M. Tian & Q. Yang, &lt;i&gt;Didymella chlamydospora&lt;/i&gt; Qian Chen & L. Cai, &lt;i&gt;Didymella gei&lt;/i&gt; Qian Chen & L. Cai, &lt;i&gt;Didymella ligulariae&lt;/i&gt; Qian Chen & L. Cai, &lt;i&gt;Didymella qilianensis&lt;/i&gt; Qian Chen & L. Cai, &lt;i&gt;Didymella uniseptata&lt;/i&gt; Qian Chen & L. Cai, &lt;i&gt;Endothia cerciana&lt;/i&gt; W. Wang. & S.F. Chen, &lt;i&gt;Leptosphaerulina miscanthi&lt;/i&gt; Qian Chen & L. Cai, &lt;i&gt;Nigrospora covidalis&lt;/i&gt; M. Raza, Qian Chen & L. Cai, &lt;i&gt;Nigrospora globospora&lt;/i&gt; M. Raza, Qian Chen & L. Cai, &lt;i&gt;Nigrospora philosophiae-doctoris&lt;/i&gt; M. Raza, Qian Chen & L. Cai, &lt;i&gt;Phytophthora transitoria&lt;/i&gt; I. Milenković, T. Májek & T. Jung, &lt;i&gt;Phytophthora panamensis&lt;/i&gt; T. Jung, Y. Balci, K. Broders & I. Milenković, &lt;i&gt;Phytophthora variabilis&lt;/i&gt; T. Jung, M. Horta Jung & I. Milenković, &lt;i&gt;Pseudocercospora delonicicola&lt;/i&gt; C. Nakash., L. Suhaizan & I. Nurul Faziha, &lt;i&gt;Pseudocercospora farfugii&lt;/i&gt; C. Nakash., I. Araki, & Ai Ito, &lt;i&gt;Pseudocercospora hardenbergiae&lt;/i&gt; Crous & C. Nakash., &lt;i&gt;Pseudocercospora kenyirana&lt;/i&gt; C. Nakash., L. Suhaizan & I. Nurul Faziha, &lt;i&gt;Pseudocercospora perrottetiae&lt;/i&gt; Crous, C. Nakash. & C.Y. Chen, &lt;i&gt;Pseudocercospora platyceriicola&lt;/i&gt; C. Nakash., Y. Hatt, L. Suhaizan & I. Nurul Faziha, &lt;i&gt;Pseudocercospora stemonicola&lt;/i&gt; C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, &lt;i&gt;Pseudocercospora terengganuensis&lt;/i&gt; C. Nakash., Y. Hatt., L. Su","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"417-564"},"PeriodicalIF":14.1,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348350","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":"Multi-locus phylogeny unmasks hidden species within the specialised spider-parasitic fungus, <i>Gibellula</i> (<i>Hypocreales, Cordycipitaceae</i>) in Thailand.","authors":"W Kuephadungphan, B Petcharad, K Tasanathai, D Thanakitpipattana, N Kobmoo, A Khonsanit, R A Samson, J J Luangsa-Ard","doi":"10.3114/sim.2022.101.04","DOIUrl":"10.3114/sim.2022.101.04","url":null,"abstract":"<p><p>Over 80 species of hypocrealean fungi are reported as pathogens of spiders and harvestmen. Among these fungi, the genus <i>Gibellula</i> is highly regarded as a specialised spider-killer that has never been reported to infect other arthropods. While more than 20 species of <i>Gibellula</i> are known, few attempts to identify the infected spiders have been made despite the fact that the host specificity can help identify the fungal species. Here, we morphologically describe and illustrate eight new species of <i>Gibellula</i> and three new records from Thailand of known species along with the multi-gene phylogeny that clearly showed the segregation among the proposed species. Examination of the <i>Gibellula</i>-infected spider hosts identified <i>Oxyopidae</i>, <i>Uloboridae</i> and, for the first time, the ant-mimicking genus <i>Myrmarachne</i>. <b>Taxonomic novelties: New species:</b> <i>Gibellula brevistipitata</i> Kuephadungphan, Tasanathai & Luangsa-ard, <i>G. longicaudata</i> Tasanathai, Kuephadungphan & Luangsa-ard, <i>G. longispora</i> Kuephadungphan & Luangsa-ard, <i>G. nigelii</i> Kuephadungphan, Tasanathai & Luangsa-ard, <i>G. parvula</i> Kuephadungphan, Tasanathai & Luangsa-ard, <i>G. pilosa</i> Kuephadungphan, Tasanathai & Luangsa-ard<i>, G. solita</i> Kuephadungphan, Tasanathai & Luangsa-ard, <i>G. trimorpha</i> Tasanathai, Khonsanit, Kuephadungphan & Luangsa-ard. <b>Citation:</b> Kuephadungphan W, Petcharad B, Tasanathai K, Thanakitpipattana D, Kobmoo N, Khonsanit A, Samson RA, Luangsa-ard JJ (2022). Multi-locus phylogeny unmasks hidden species within the specialised spider-parasitic fungus, <i>Gibellula</i> (<i>Hypocreales</i>, <i>Cordycipitaceae</i>) in Thailand. <i>Studies in Mycology</i> <b>101</b>: 245-286. doi: 10.3114/sim.2022.101.04.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"245-286"},"PeriodicalIF":3.784,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348349","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":"Updating species diversity of <i>Colletotrichum</i>, with a phylogenomic overview.","authors":"F Liu,&nbsp;Z Y Ma,&nbsp;L W Hou,&nbsp;Y Z Diao,&nbsp;W P Wu,&nbsp;U Damm,&nbsp;S Song,&nbsp;L Cai","doi":"10.3114/sim.2022.101.01","DOIUrl":"https://doi.org/10.3114/sim.2022.101.01","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The genus &lt;i&gt;Colletotrichum&lt;/i&gt; includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated &lt;i&gt;Colletotrichum&lt;/i&gt; species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 &lt;i&gt;Colletotrichum&lt;/i&gt; strains isolated from plants representing 322 species from 248 genera, or air and soil samples, from 87 locations in China, as well as 56 strains from Saudi Arabia, Thailand, Turkey, and the UK. Based on morphological characteristics and multi-locus phylogenetic analyses, the strains were assigned to 107 species, including 30 new species described in this paper and 18 new records for China. The currently most comprehensive backbone tree of &lt;i&gt;Colletotrichum&lt;/i&gt;, comprising 16 species complexes (including a newly introduced &lt;i&gt;C. bambusicola&lt;/i&gt; species complex) and 15 singleton species, is provided. Based on these analyses, 280 species with available molecular data are accepted in this genus, of which 139 have been reported in China, accounting for 49.6 % of the species. &lt;i&gt;Colletotrichum siamense&lt;/i&gt;, &lt;i&gt;C. karsti&lt;/i&gt;, &lt;i&gt;C. fructicola&lt;/i&gt;, &lt;i&gt;C. truncatum&lt;/i&gt;, &lt;i&gt;C. fioriniae&lt;/i&gt;, and &lt;i&gt;C. gloeosporioides&lt;/i&gt; were the most commonly detected species in China, as well as the species with the broadest host range. By contrast, 76 species were currently found to be associated with a single plant species or genus in China. To date, 33 &lt;i&gt;Colletotrichum&lt;/i&gt; species have been exclusively reported as endophytes. Furthermore, we generated and assembled whole-genome sequences of the 30 new and a further 18 known species. The most comprehensive genome tree comprising 94 &lt;i&gt;Colletotrichum&lt;/i&gt; species based on 1 893 single-copy orthologous genes was hence generated, with all nodes, except four, supported by 100 % bootstrap values. Collectively, this study represents the most comprehensive investigation of &lt;i&gt;Colletotrichum&lt;/i&gt; diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus. &lt;b&gt;Taxonomic novelties: New species:&lt;/b&gt; &lt;i&gt;Colletotrichum arecacearum&lt;/i&gt; F. Liu, Z.Y. Ma & L. Cai, &lt;i&gt;Colletotrichum bicoloratum&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotrichum bromeliacearum&lt;/i&gt; F. Liu & L. Cai, &lt;i&gt;Colletotrichum buxi&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotrichum chamaedoreae&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotrichum crousii&lt;/i&gt; F. Liu, Z.Y. Ma & L. Cai, &lt;i&gt;Colletotrichum danxiashanense&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotrichum diversisporum&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotrichum diversum&lt;/i&gt; F. Liu & L. Cai, &lt;i&gt;Colletotrichum dolichoconidiophori&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotrichum iris&lt;/i&gt; F. Liu & L. Cai, &lt;i&gt;Colletotrichum monsterae&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotrichum multiseptatum&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotrichum nageiae&lt;/i&gt; F. Liu, W.P. Wu & L. Cai, &lt;i&gt;Colletotr","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"1-56"},"PeriodicalIF":16.5,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348347","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":"Generic boundaries in the <i>Ophiostomatales</i> reconsidered and revised.","authors":"Z W de Beer,&nbsp;M Procter,&nbsp;M J Wingfield,&nbsp;S Marincowitz,&nbsp;T A Duong","doi":"10.3114/sim.2022.101.02","DOIUrl":"https://doi.org/10.3114/sim.2022.101.02","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The &lt;i&gt;Ophiostomatales&lt;/i&gt; was erected in 1980. Since that time, several of the genera have been redefined and others have been described. There are currently 14 accepted genera in the Order. They include species that are the causal agents of plant and human diseases and common associates of insects such as bark beetles. Well known examples include the Dutch elm disease fungi and the causal agents of sporotrichosis in humans and animals. The taxonomy of the &lt;i&gt;Ophiostomatales&lt;/i&gt; was confused for many years, mainly due to the convergent evolution of morphological characters used to delimit unrelated fungal taxa. The emergence of DNA-based methods has resolved much of this confusion. However, the delineation of some genera and the placement of various species and smaller lineages remains inconclusive. In this study we reconsidered the generic boundaries within the &lt;i&gt;Ophiostomatales&lt;/i&gt;. A phylogenomic framework constructed from genome-wide sequence data for 31 species representing the major genera in the Order was used as a guide to delineate genera. This framework also informed our choice of the best markers from the currently most commonly used gene regions for taxonomic studies of these fungi. DNA was amplified and sequenced for more than 200 species, representing all lineages in the Order. We constructed phylogenetic trees based on the different gene regions and assembled a concatenated data set utilising a suite of phylogenetic analyses. The results supported and confirmed the delineation of nine of the 14 currently accepted genera, &lt;i&gt;i.e.&lt;/i&gt; &lt;i&gt;Aureovirgo, Ceratocystiopsis, Esteya, Fragosphaeria, Graphilbum, Hawksworthiomyces, Ophiostoma, Raffaelea&lt;/i&gt; and &lt;i&gt;Sporothrix&lt;/i&gt;. The two most recently described genera, &lt;i&gt;Chrysosphaeria&lt;/i&gt; and &lt;i&gt;Intubia&lt;/i&gt;, were not included in the multi-locus analyses. This was due to their high sequence divergence, which was shown to result in ambiguous taxonomic placement, even though the results of phylogenomic analysis supported their inclusion in the &lt;i&gt;Ophiostomatales&lt;/i&gt;. In addition to the currently accepted genera in the &lt;i&gt;Ophiostomatales&lt;/i&gt;, well-supported lineages emerged that were distinct from those genera. These are described as novel genera. Two lineages included the type species of &lt;i&gt;Grosmannia&lt;/i&gt; and &lt;i&gt;Dryadomyces&lt;/i&gt; and these genera are thus reinstated and their circumscriptions redefined. The descriptions of all genera in the &lt;i&gt;Ophiostomatales&lt;/i&gt; were standardised and refined where this was required and 39 new combinations have been provided for species in the newly emerging genera and one new combination has been provided for &lt;i&gt;Sporothrix&lt;/i&gt;. The placement of &lt;i&gt;Afroraffaelea&lt;/i&gt; could not be confirmed using the available data and the genus has been treated as &lt;i&gt;incertae sedis&lt;/i&gt; in the &lt;i&gt;Ophiostomatales&lt;/i&gt;. &lt;i&gt;Paleoambrosia&lt;/i&gt; was not included in this study, due to the absence of living material available for this monotypic fossil genus. Overall, this study has pro","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"57-120"},"PeriodicalIF":16.5,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348345","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}