K Glässnerová, F Sklenář, Ž Jurjević, J Houbraken, T Yaguchi, C M Visagie, J Gené, J P Z Siqueira, A Kubátová, M Kolařík, V Hubka
Aspergillus section Candidi 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 Candidi 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 (benA, CaM and RPB2) 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 (A. magnus and A. tenebricus). In addition, we proposed the new name A. neotritici to replace an invalidly described A. tritici. The revised section Candidi now encompasses nine species, some of which manifest a high level of intraspecific genetic and/or phenotypic variability (e.g., A. subalbidus and A. campestris) while others are more uniform (e.g., A. candidus or A. pragensis). 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. Taxonomic novelties: New species:Aspergillus magnus Glässnerová & Hubka; Aspergillus neotritici Glässnerová & Hubka; Aspergillus tenebricus Houbraken, Glässnerová & Hubka. Citation: 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 Aspergillus section Candidi. Studies in Mycology102: 1-51. doi: 10.3114/sim.2022.102.01.
{"title":"A monograph of <i>Aspergillus</i> section <i>Candidi</i>.","authors":"K Glässnerová, F Sklenář, Ž Jurjević, J Houbraken, T Yaguchi, C M Visagie, J Gené, J P Z Siqueira, A Kubátová, M Kolařík, 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}
Pub Date : 2022-12-01Epub Date: 2022-12-19DOI: 10.3114/sim.2022.102.03
C Bian, Y Kusuya, F Sklenář, E D'hooge, T Yaguchi, S Ban, C M Visagie, J Houbraken, H Takahashi, V Hubka
<p><p>The <i>Aspergillus</i> series <i>Nigri</i> 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 (<i>benA</i>, <i>CaM</i> and <i>RPB2</i>) for 276 strains from series <i>Nigri</i> 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: <i>A. niger</i>, <i>A. tubingensis</i> and <i>A. brasiliensis</i>. 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 <i>benA</i>, <i>CaM</i> and <i>RPB2</i> 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 <i>A. niger</i> and <i>A. brasiliensis</i> lineages, while one to four species were inconsistently delimited in the <i>A. tubingensis</i> lineage. After considering all of these results and their practical implications, we propose that the revised series <i>Nigri</i> includes six species: <i>A. brasiliensis</i>, <i>A. eucalypticola</i>, <i>A. luchuensis</i> (syn<i>. A. piperis</i>), <i>A. niger</i> (syn. <i>A. vinaceus</i> and <i>A. welwitschiae</i>), <i>A. tubingensis</i> (syn. <i>A. chiangmaiensis</i>, <i>A. costaricensis</i>, <i>A. neoniger</i> and <i>A. pseudopiperis</i>) and <i>A. vadensis</i>. We also showed that the intraspecific genetic variability in the redefined <i>A. niger</i> and <i>A. tubingensis</i> 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. <b>Cita
黑曲霉（Aspergillus）系列包含生物技术和医学上的重要菌种。它们可以产生有害的霉菌毒素，这与这些菌种经常出现在食品和室内环境中有关。该系列的分类法经历了多次重新整理，目前该系列共有 14 个物种，其中大多数被认为是隐性物种。然而，即使使用 DNA 测序法或 MALDI-TOF 质谱法，许多分离物的种级鉴定仍存在问题或无法鉴定，这表明在物种界限的定义上可能存在问题，或存在未描述的物种多样性。为了重新研究物种界限，我们收集了尼格里系列中 276 个菌株的三个系统发育标记（benA、CaM 和 RPB2）的 DNA 序列，并生成了 18 个新的全基因组序列。利用三基因数据集，我们采用了基于多物种凝聚模型的系统发生方法，包括四种单焦点方法（GMYC、bGMYC、PTP 和 bPTP）和一种多焦点方法（STACEY）。在总共 15 种方法及其各种设置中，有 11 种只支持识别与三个主要系统发生系相对应的三个物种：A. niger、A. tubingensis 和 A. brasiliensis。同样，GCPSR 方法（谱系一致系统发育物种识别）和 DELINEATE 软件的分析也支持识别这三个物种。我们还发现，基于 benA、CaM 和 RPB2 的系统发生是次优的，与使用 5 752 个单拷贝直向同源蛋白构建的系统发生存在显著差异；因此，划分方法的结果可能会受到比通常水平更高的不确定性的影响。为了克服这一问题，我们从这些基因组中随机选择了 200 个基因，进行了 10 次独立的 STACEY 分析，每次分析 20 个基因。所有分析结果都支持在 A. niger 和 A. brasiliensis 支系中只识别一个物种，而在 A. tubingensis 支系中则不一致地划分出一至四个物种。在考虑了所有这些结果及其实际影响后，我们建议修订后的 Nigri 系列包括 6 个种：A. brasiliensis、A. eucalypticola、A. luchuensis（与 A. piperis 同源）、A. niger（与 A. vinaceus 和 A. welwitschiae 同源）、A. tubingensis（与 A. chiangmaiensis、A. costaricensis、A. neoniger 和 A. pseudopiperis 同源）和 A. vadensis。我们还发现，重新定义的 A. niger 和 A. tubingensis 的种内遗传变异性与其他天青霉菌中常见的遗传变异性并无差异。我们在研究中补充了一份已被接受的种、异名和未解决名称的清单，其中一些名称可能会威胁到当前分类法的稳定性。引用：Bian C, Kusuya Y, Sklenář F, D'hooge E, Yaguchi T, Ban S, Visagie CM, Houbraken J, Takahashi H, Hubka V (2022)。减少黑曲霉系列中可接受菌种的数量。Doi: 10.3114/sim.2022.102.03.
{"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":"<p><p>The <i>Aspergillus</i> series <i>Nigri</i> 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 (<i>benA</i>, <i>CaM</i> and <i>RPB2</i>) for 276 strains from series <i>Nigri</i> 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: <i>A. niger</i>, <i>A. tubingensis</i> and <i>A. brasiliensis</i>. 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 <i>benA</i>, <i>CaM</i> and <i>RPB2</i> 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 <i>A. niger</i> and <i>A. brasiliensis</i> lineages, while one to four species were inconsistently delimited in the <i>A. tubingensis</i> lineage. After considering all of these results and their practical implications, we propose that the revised series <i>Nigri</i> includes six species: <i>A. brasiliensis</i>, <i>A. eucalypticola</i>, <i>A. luchuensis</i> (syn<i>. A. piperis</i>), <i>A. niger</i> (syn. <i>A. vinaceus</i> and <i>A. welwitschiae</i>), <i>A. tubingensis</i> (syn. <i>A. chiangmaiensis</i>, <i>A. costaricensis</i>, <i>A. neoniger</i> and <i>A. pseudopiperis</i>) and <i>A. vadensis</i>. We also showed that the intraspecific genetic variability in the redefined <i>A. niger</i> and <i>A. tubingensis</i> 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. <b>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}
P Baldrian, L Bell-Dereske, C Lepinay, T Větrovský, P Kohout
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. Citation: Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. Studies in Mycology103: 1-24. doi: 10.3114/sim.2022.103.01.
{"title":"Fungal communities in soils under global change.","authors":"P Baldrian, L Bell-Dereske, C Lepinay, T Větrovský, 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 CO<sub>2</sub> 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}
Pub Date : 2022-09-01Epub Date: 2022-10-18DOI: 10.3114/sim.2022.103.02
A Telagathoti, M Probst, E Mandolini, U Peintner
<p><p>Fungi are incredibly diverse, but they are unexplored, especially in the subalpine and alpine zone. <i>Mortierellaceae</i> 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 <i>Mortierellaceae</i> was recently resolved based on current state of the art molecular techniques, and the paraphyletic genus <i>Mortierella sensu lato</i> (<i>s.l.</i>) was divided into 13 monophyletic genera. Our extensive sampling campaigns in the Austrian Alps resulted in 139 different <i>Mortierellaceae</i> 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 (<i>RPB1</i>). In this study, we proposed a new genus and described 13 new species belonging to the genera <i>Entomortierella</i>, <i>Linnemannia</i>, <i>Mortierella</i> and <i>Podila</i>. In addition, we proposed eight new combinations, re-defined <i>E. jenkinii</i> at species level, defined a neotype for <i>M. alpina</i> and lecto- as well as epitypes for <i>M. fatshederae</i>, <i>M. jenkinii,</i> and <i>M. longigemmata.</i> 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 <i>Mortierellaceae</i>, 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. <b>Taxonomic novelties:</b> <b>new genus:</b> <i>Tyroliella</i> Telagathoti, Probst & Peintner; <b>New species:</b> <i>Entomortierella galaxiae</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia bainierella</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia stellaris</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia nimbosa</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia mannui</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia friederikiana</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia scordiella</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia solitaria</i> Telagathoti, M. Probst & Peintner, <i>Mortierella triangularis</i> Telagathoti, M. Probst & Peintner, <i>Mortierella lapis</i> Telagathoti, M. Probst & Peintner, <i>Podila himami</i> Telagathoti, M. Probst & Peintner, <i>Podila occulta</i> Telagathoti, M. Probst & Peintner, <i>Tyroliella animus-liberi</i> Telagathoti, Probst & Peintner; <b>New combinations:</b> <i>Entomortierella basiparvispora</i> (W. Gams & Grinb.) Telagathoti, M. Probst & Peintner, <i>Entomortierella jenkinii</i> (A.L. Sm.
真菌的多样性令人难以置信，但它们尚未被开发，尤其是在亚高山和高寒地带。毛蕊花科（Mortierellaceae）无疑是陆地栖息地（包括亚高山和高寒地带）中数量最多、物种最丰富、分布最广的可栽培土壤真菌科之一。根据目前最先进的分子技术，最近对毛蕊花科的系统发育进行了解析，并将旁系的毛蕊花属（mortierella sensu lato，s.l.）划分为 13 个单系属。我们在奥地利阿尔卑斯山进行了广泛的采样活动，获得了 139 个不同的毛蕊花科纯培养分离物，代表 13 个新种。在定义类群时，我们采用了经典的形态学标准和基于 DNA 的现代方法。根据核糖体 DNA 内部转录间隔（rDNA ITS）、大亚基（LSU）和 DNA 引导的 RNA 聚合酶 II 最大亚基 1（RPB1）确定了系统发育关系。在这项研究中，我们提出了一个新属，并描述了属于 Entomortierella 属、Linnemannia 属、Mortierella 属和 Podila 属的 13 个新种。此外，我们还提出了 8 个新的组合，将 E. jenkinii 重新定义为种，为 M. alpina 和 lecto- 定义了新模式，并为 M. fatshederae、M. jenkinii 和 M. longigemmata 定义了表型。rDNA ITS 区域通常被用作真菌的经典条形码基因。然而，所获得的系统发育分辨率往往过低，无法准确鉴定毛蕊花科的近缘种，尤其是在取样量较小的情况下。在这种情况下，可以根据纯培养分离物的形态特征进行明确鉴定。因此，我们还提供了系统发生系内物种鉴定的二分法。分类学新发现：新属：Tyroliella Telagathoti, Probst & Peintner；新种：Entomortierella galaxiae Telagathoti, M. Probst & Peintner, Linnemannia bainierella Telagathoti, M. Probst & Peintner, Linnemannia stellaris Telagathoti, M. Probst & Peintner, Linnemannia nimbosa Telagathoti, M. Probst & Peintner, Linnemannia nimbosa Telagathoti, M. Probst & Peintner.Probst & Peintner, Linnemannia mannui Telagathoti, M. Probst & Peintner, Linnemannia friederikiana Telagathoti, M. Probst & Peintner, Linnemannia scordiella Telagathoti, M. Probst & Peintner, Linnemannia stellaris Telagathoti, M. Probst & Peintner, Linnemannia nimbosa Telagathoti, M.Probst & Peintner, Linnemannia solitaria Telagathoti, M. Probst & Peintner, Mortierella triangularis Telagathoti, M. Probst & Peintner, Mortierella lapis Telagathoti, M.Probst & Peintner, Podila himami Telagathoti, M. Probst & Peintner, Podila occulta Telagathoti, M. Probst & Peintner, Tyroliella animus-liberi Telagathoti, Probst & Peintner; New combinations：Entomortierella basiparvispora (W. Gams & Grinb.) Telagathoti, M. Probst & Peintner, Entomortierella jenkinii (A.L. Sm.) Telagathoti, M. Probst & Peintner; Entomortierella sugadairana (Y. Takash. et al.) Telagathoti, M. Probst & Peintner, Linnemannia zonata (Linnem. ex W. Gams) Telagathoti, M. Probst & Peintner.Probst & Peintner, Linnemannia fluviae （Hyang B. Lee et al.Probst & Peintner, Linnemannia cogitans (Degawa) Telagathoti, M. Probst & Peintner, Tyroliella pseudozygospora (W. Gams & Carreiro) Telagathoti, M. Probst & Peintner; Epitypifications (basionyms)：Mortierella bainieri var.Neotypification (basionym)：Mortierella alpina Peyronel.引用：Telagathoti A, Probst M, Mandolini E, Peintner U (2022).来自亚高山和高山栖息地的毛地黄科：新种 Entomortierella、Linnemannia、Mortierella、Podila 和 Tyroliella gen.Doi: 10.3114/sim.2022.103.02.
{"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":"<p><p>Fungi are incredibly diverse, but they are unexplored, especially in the subalpine and alpine zone. <i>Mortierellaceae</i> 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 <i>Mortierellaceae</i> was recently resolved based on current state of the art molecular techniques, and the paraphyletic genus <i>Mortierella sensu lato</i> (<i>s.l.</i>) was divided into 13 monophyletic genera. Our extensive sampling campaigns in the Austrian Alps resulted in 139 different <i>Mortierellaceae</i> 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 (<i>RPB1</i>). In this study, we proposed a new genus and described 13 new species belonging to the genera <i>Entomortierella</i>, <i>Linnemannia</i>, <i>Mortierella</i> and <i>Podila</i>. In addition, we proposed eight new combinations, re-defined <i>E. jenkinii</i> at species level, defined a neotype for <i>M. alpina</i> and lecto- as well as epitypes for <i>M. fatshederae</i>, <i>M. jenkinii,</i> and <i>M. longigemmata.</i> 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 <i>Mortierellaceae</i>, 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. <b>Taxonomic novelties:</b> <b>new genus:</b> <i>Tyroliella</i> Telagathoti, Probst & Peintner; <b>New species:</b> <i>Entomortierella galaxiae</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia bainierella</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia stellaris</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia nimbosa</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia mannui</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia friederikiana</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia scordiella</i> Telagathoti, M. Probst & Peintner, <i>Linnemannia solitaria</i> Telagathoti, M. Probst & Peintner, <i>Mortierella triangularis</i> Telagathoti, M. Probst & Peintner, <i>Mortierella lapis</i> Telagathoti, M. Probst & Peintner, <i>Podila himami</i> Telagathoti, M. Probst & Peintner, <i>Podila occulta</i> Telagathoti, M. Probst & Peintner, <i>Tyroliella animus-liberi</i> Telagathoti, Probst & Peintner; <b>New combinations:</b> <i>Entomortierella basiparvispora</i> (W. Gams & Grinb.) Telagathoti, M. Probst & Peintner, <i>Entomortierella jenkinii</i> (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}
L Quijada, H O Baral, P R Johnston, K Pärtel, J K Mitchell, T Hosoya, H Madrid, T Kosonen, S Helleman, E Rubio, E Stöckli, S Huhtinen, D H Pfister
In a recently published classification scheme for Leotiomycetes, the new family Hyphodiscaceae 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 Hyphodiscaceae is provided, notes and descriptions of the included genera are supplied, and keys to genera and species in Hyphodiscaceae are supplied. Microscypha cajaniensis is combined in Hyphodiscus, and Scolecolachnum nigricans is a taxonomic synonym of Fuscolachnum pteridis. Future work in this family should focus on increasing phylogenetic sampling outside of Eurasia and better characterising described species to help resolve outstanding issues. Citation: 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 Hyphodiscaceae. Studies in Mycology103: 59-85. doi: 10.3114/sim.2022.103.03.
{"title":"A review of <i>Hyphodiscaceae</i>.","authors":"L Quijada, H O Baral, P R Johnston, K Pärtel, J K Mitchell, T Hosoya, H Madrid, T Kosonen, S Helleman, E Rubio, E Stöckli, S Huhtinen, 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}
M Réblová, M Hernández-Restrepo, F Sklenář, J Nekvindová, K Réblová, M Kolařík
<p><p><i>Chloridium</i> 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, <i>i.e.</i> <i>Chloridium</i>, <i>Gongromeriza</i>, and <i>Psilobotrys</i>. Sexual morphs have been placed in the widely perceived genus <i>Chaetosphaeria</i>, 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 <i>Chloridium</i> is polyphyletic, and the original sections are not congeneric. Therefore, we abolish the existing classification and propose to restore the generic status of <i>Gongromeriza</i> and <i>Psilobotrys</i>. We present a new generic concept and define <i>Chloridium</i> as a monophyletic, polythetic genus comprising 37 species distributed in eight sections. In addition, of the taxa earlier referred to <i>Gongromeriza</i>, two have been redisposed to the new genus <i>Gongromerizella</i>. Analysis of published metabarcoding data showed that <i>Chloridium</i> 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 <i>Chloridium</i> 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. <b>Taxonomic novelties:</b> <b>New genus:</b> <i>Gongromerizella</i> Réblová; <b>New sections:</b> <i>Chloridium</i> section <i>Cryptogonytrichum</i> Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, <i>Chloridium</i> section <i>Gonytrichopsis</i> Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, <i>Chloridium</i> section <i>Metachloridium</i> Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, <i>Chloridium</i> section <i>Volubilia</i> Réblová, Hern.-Restr., M. Kolařík & F. Sklenar; <b>New species:</b> <i>Chloridium</i> <i>bellum</i> Réblová & Hern.-Restr., <i>Chloridium biforme</i> Réblová & Hern.-Restr., <i>Chloridium detriticola</i> Réblová & Hern.-Restr., <i>Chloridium</i> <i>gamsii</i> Réblová & Hern.-Restr., <i>Chloridium guttiferum</i> Réblová & Hern.-Restr., <i>Chloridium</i> <i>moratum</i> Réblo
梭菌是一种很少被研究的土壤和木材中居住的真菌，它们在多个位点上共享一种罕见的亲性孢子生模式。该属在历史上被分为三个形态部分，即clooridium, Gongromeriza和Psilobotrys。有性形态被放置在广泛感知的Chaetosphaeria属中，但与它们的无性对应物不同，它们表现出很少或没有形态变化。最近的分子研究扩大了一般概念，包括一组新的形态特征定义的物种，如颈状菌丝、刚毛、离散的分生孢子和青霉分枝的分生孢子。该研究基于分子物种划分方法、系统发育分析、祖先状态重建、形态假设和全球生物地理分析的一致性。多位点系统发育表明，经典的氯藻概念是多系性的，原始片段不具有同源性。因此，我们取消现有的分类，并建议恢复贡罗梅属和Psilobotrys属的地位。我们提出了一个新的属的概念，并定义为一个单系，合成属包括37种分布在8个区段。此外，在先前提到的贡罗merizella分类群中，有两个被重新定位为贡罗merizella新属。对已发表的元条形码数据的分析表明，在GlobalFungi数据库中保存的环境样品中，氯酸菌是一种常见的土壤真菌，占序列reads的很大比例(0.3%)。分析还表明，它们通常与森林栖息地有关，它们的分布受到气候的强烈影响，我们关于它们在不同温度下生长能力的数据证实了这一点。我们证明了氯酸菌形成物种特定的分布范围，这在微观土壤真菌中很少有记录。本研究表明，利用全球真菌数据库研究真菌的生物地理学和生态学是可行的。分类新颖性:新属:Gongromerizella r blov;新科:氯虫科，隐虫科，Hern.-Restr。， M. Kolařík & F. Sklenar, chroridium section Gonytrichopsis r blov， Hern.-Restr。， M. Kolařík & F. Sklenar, chroridium section r blov， hern . restr。， M. Kolařík & F. Sklenar, chroridium section Volubilia r blov， hern . restr。， M. Kolařík & F. Sklenar;新种:紫藻(cloridium bellum) r blov & hern . restr。;;;;;;;;;;;;;;;，甘氏氯虫r - blov & Hern.-Restr。，氯化铯r blov和Hern.-Restr。， moratum r blov & hern . restr。[j] .中国农业大学学报(自然科学版)，新泽兰芽孢杆菌r - blov;，伸长梭状芽孢杆菌r blov & Hern.-Restr。;;;;;;新变种:黄体衣藻(cloridium bellum var. luteum)、r blov和hern . restr。[j] .豆瓣藻变种积液r blov;* * * * * * * * *;新组合:choridium section Gonytrichum (Nees & T. Nees) r blov， Hern.-Restr。， M. Kolařík & F. Sklenar, chlordium section Mesobotrys (Sacc.)Reblova Hern.-Restr。， M. Kolařík & F. Sklenar, pseudophhialocephala (M.S. Calabon et al.);， M. Kolařík和F. Sklenar，氯气的明喻(W. Gams & Hol.-Jech.)r blov & Hern.-Restr。——氯化氯化钠(W. Gams & Hol.-Jech)r blov & Hern.-Restr。亚球状氯酸菌(W. Gams & Hol.-Jech)r blov & Hern.-Restr。，褐梭菌(Corda) r blov & Hern.-Restr。，绿孢杆菌(cloridium ypsilosporum)r blov & Hern.-Restr。(G. Weber et al.) r blov & hern . restr。刘宁刚等。r blov & Hern.-Restr。，筒孢镰刀孢菌(W. Gams & Hol.-Jech)r blov， Gongromeriza pygmaea (P. Karst.)r blov， Gongromerizella lignicola (F. Mangenot) r blov， Gongromerizella pachytrachela (W. Gams & hole .- jech) r blov， Gongromerizella pini (croous & Akulov) r blov;新名称:透明氯离子r blov & hern . restr;(基本名):fusca Corda毛藻，Gonytrichum caesium var. subglobosum W. Gams & hole .- jech;卵形分型(基底):Gonytrichum caesium Nees & T. Nees。引文来源:r blov M, Hernández-Restrepo M, Sklenář F, nekvindov J, r blov K, Kolařík M(2022)。氯藻的巩固:新分类为8科37种，并恢复了龙葵属和龙葵属。真菌学研究103:87-212。doi: 10.3114 / sim.2022.103.04。
{"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, M Hernández-Restrepo, F Sklenář, J Nekvindová, K Réblová, M Kolařík","doi":"10.3114/sim.2022.103.04","DOIUrl":"https://doi.org/10.3114/sim.2022.103.04","url":null,"abstract":"<p><p><i>Chloridium</i> 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, <i>i.e.</i> <i>Chloridium</i>, <i>Gongromeriza</i>, and <i>Psilobotrys</i>. Sexual morphs have been placed in the widely perceived genus <i>Chaetosphaeria</i>, 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 <i>Chloridium</i> is polyphyletic, and the original sections are not congeneric. Therefore, we abolish the existing classification and propose to restore the generic status of <i>Gongromeriza</i> and <i>Psilobotrys</i>. We present a new generic concept and define <i>Chloridium</i> as a monophyletic, polythetic genus comprising 37 species distributed in eight sections. In addition, of the taxa earlier referred to <i>Gongromeriza</i>, two have been redisposed to the new genus <i>Gongromerizella</i>. Analysis of published metabarcoding data showed that <i>Chloridium</i> 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 <i>Chloridium</i> 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. <b>Taxonomic novelties:</b> <b>New genus:</b> <i>Gongromerizella</i> Réblová; <b>New sections:</b> <i>Chloridium</i> section <i>Cryptogonytrichum</i> Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, <i>Chloridium</i> section <i>Gonytrichopsis</i> Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, <i>Chloridium</i> section <i>Metachloridium</i> Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, <i>Chloridium</i> section <i>Volubilia</i> Réblová, Hern.-Restr., M. Kolařík & F. Sklenar; <b>New species:</b> <i>Chloridium</i> <i>bellum</i> Réblová & Hern.-Restr., <i>Chloridium biforme</i> Réblová & Hern.-Restr., <i>Chloridium detriticola</i> Réblová & Hern.-Restr., <i>Chloridium</i> <i>gamsii</i> Réblová & Hern.-Restr., <i>Chloridium guttiferum</i> Réblová & Hern.-Restr., <i>Chloridium</i> <i>moratum</i> 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}
Pub Date : 2022-07-01Epub Date: 2022-06-02DOI: 10.3114/sim.2022.101.06
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
<p><p>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 <i>Ascochyta</i>, <i>Cadophora</i>, <i>Celoporthe</i>, <i>Cercospora</i>, <i>Coleophoma</i>, <i>Cytospora</i>, <i>Dendrostoma</i>, <i>Didymella</i>, <i>Endothia</i>, <i>Heterophaeomoniella, Leptosphaerulina</i>, <i>Melampsora</i>, <i>Nigrospora</i>, <i>Pezicula</i>, <i>Phaeomoniella</i>, <i>Pseudocercospora</i>, <i>Pteridopassalora, Zymoseptoria</i>, and one genus of oomycetes, <i>Phytophthora</i>. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names. <b>Taxonomic novelties: New genera:</b> <i>Heterophaeomoniella</i> L. Mostert, C.F.J. Spies, Halleen & Gramaje, <i>Pteridopassalora</i> C. Nakash. & Crous; <b>New species:</b> <i>Ascochyta flava</i> Qian Chen & L. Cai, <i>Cadophora domestica</i> L. Mostert, R. van der Merwe, Halleen & Gramaje, <i>Cadophora rotunda</i> L. Mostert, R. van der Merwe, Halleen & Gramaje, <i>Cadophora vinacea</i> J.R. Úrbez-Torres, D.T. O'Gorman & Gramaje, <i>Cadophora vivarii</i> L. Mostert, Havenga, Halleen & Gramaje, <i>Celoporthe foliorum</i> H. Suzuki, Marinc. & M.J. Wingf., <i>Cercospora alyssopsidis</i> M. Bakhshi, Zare & Crous, <i>Dendrostoma elaeocarpi</i> C.M. Tian & Q. Yang, <i>Didymella chlamydospora</i> Qian Chen & L. Cai, <i>Didymella gei</i> Qian Chen & L. Cai, <i>Didymella ligulariae</i> Qian Chen & L. Cai, <i>Didymella qilianensis</i> Qian Chen & L. Cai, <i>Didymella uniseptata</i> Qian Chen & L. Cai, <i>Endothia cerciana</i> W. Wang. & S.F. Chen, <i>Leptosphaerulina miscanthi</i> Qian Chen & L. Cai, <i>Nigrospora covidalis</i> M. Raza, Qian Chen & L. Cai, <i>Nigrospora globospora</i> M. Raza, Qian Chen & L. Cai, <i>Nigrospora philosophiae-doctoris</i> M. Raza, Qian Chen & L. Cai, <i>Phytophthora transitoria</i> I. Milenković, T. Májek & T. Jung, <i>Phytophthora panamensis</i> T. Jung, Y. Balci, K. Broders & I. Milenković, <i>Phytophthora variabilis</i> T. Jung, M. Horta Jung & I. Milenković, <i>Pseudocercospora delonicicola</i> C. Nakash., L. Suhaizan & I. Nurul Faziha, <i>Pseudocercospora farfugii</i> C. Nakash., I. Araki, & Ai Ito, <i>Pseudocercospora hardenbergiae</i> Crous & C. Nakash., <i>Pseudocercospora kenyirana</i> C. Nakash., L. Suhaizan & I. Nurul Faziha, <i>Pseudocercospora perrottetiae</i> Crous, C. Nakash. & C.Y. Chen, <i>Pseudocercospora platyceriicola</i> C. Nakash., Y. Hatt, L. Suhaizan & I. Nurul Faziha, <i>Pseudocercospora stemonicola</i> C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, <i>Pseudocercospora terengganuensis</i> C. Nakash., Y. Hatt., L. Su
本文是《植物病原真菌属》（GOPHY）系列的第四篇论文。该系列提供了所涉及类群的形态描述、病理、分布、寄主和疾病症状等信息，以及 DNA 条形码。此外，该系列还提供了所涉及属中 12 个模式种或新种的全基因组序列。Didymella、Endothia、Heterophaeomoniella、Leptosphaerulina、Melampsora、Nigrospora、Pezicula、Phaeomoniella、Pseudocercospora、Pteridopassalora、Zymoseptoria 以及一个卵菌属 Phytophthora。这项研究包括 2 个新属、30 个新种、5 个新组合和 43 个旧名的分型。分类学上的新发现：新属：Heterophaeomoniella L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pteridopassalora C. Nakash. & Crous；新种：新种：Ascochyta flava Qian Chen & L. Cai, Cadophora domestica L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora rotunda L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora vinacea J. Nakash.R. Úrbez-Torres, D.T. O'Gorman & Gramaje, Cadophora vivarii L. Mostert, Havenga, Halleen & Gramaje, Celoporthe foliorum H. Suzuki, Marinc. & M.J. Wingf、Cercospora alyssopsidis M. Bakhshi, Zare & Crous, Dendrostoma elaeocarpi C.M. Tian & Q. Yang, Didymella chlamydospora Qian Chen & L. Cai, Didymella gei Qian Chen & L. Cai, Didymella ligydospora Qian Chen & L. Cai, Didymella ligydospora M. Bakhshi, Zare & Crous.Cai, Didymella ligulariae Qian Chen & L. Cai, Didymella qilianensis Qian Chen & L. Cai, Didymella uniseptata Qian Chen & L. Cai, Endothia cerciana W. Wang. & S.F. Chen.钱晨、蔡丽萍，祁连藻，单端藻 钱晨、蔡丽萍，芹菜内卷孢菌 W. Wang. & S.F. Chen，褐藻内卷孢菌 Leptosphaerulina miscanthiCai, Phytophthora transitoria I. Milenković, T. Májek & T. Jung, Phytophthora panamensis T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora variabilis T. Jung, M. Horta Jung & I. Milenković, Pseudocercospora delonicicola C. Nakash、L. Suhaizan & I. Nurul Faziha, Pseudocercospora farfugii C. Nakash、I. Araki, & Ai Ito，Pseudocercospora hardenbergiae Crous & C. Nakash.，Pseudocercospora kenyirana C. Nakash.，L. Suhaizan & I. Nurul Faziha，Pseudocercospora perrottetiae Crous, C. Nakash. & C.Y. Chen，Pseudocercospora platyceriicola C. Nakash、Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora stemonicola C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora terengganuensis C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora xenopunicae Crous & C. Nakash.; New combinations：Heterophaeomoniella pinifoliorum (Hyang B. Lee et al.) L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pseudocercospora pruni-grayanae (Sawada) C. Nakash.Kobay., Pteridopassalora nephrolepidicola (Crous & R.G. Shivas) C. Nakash. & Crous, Pteridopassalora lygodii (Goh & W.H. Hsieh) C. Nakash. & Crous; Typification：Epitypification：Botrytis infestans Mont.、Cercospora abeliae Katsuki、Cercospora ceratoniae Pat. & Trab.、Cercospora cladrastidis Jacz.、Cercospora cryptomeriicola Sawada、Cercospora dalbergiae S.H. Sun、Cercospora ebulicola W. Yamam.、Cercospora formosana W. Yamam.、Cercospora fukuii W. Yamam.Yamam., Cercospora glochidionis Sawada, Cercospora ixorana J.M. Yen & Lim, Cercospora liquidambaricola J.M. Yen, Cercospor
{"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":"<p><p>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 <i>Ascochyta</i>, <i>Cadophora</i>, <i>Celoporthe</i>, <i>Cercospora</i>, <i>Coleophoma</i>, <i>Cytospora</i>, <i>Dendrostoma</i>, <i>Didymella</i>, <i>Endothia</i>, <i>Heterophaeomoniella, Leptosphaerulina</i>, <i>Melampsora</i>, <i>Nigrospora</i>, <i>Pezicula</i>, <i>Phaeomoniella</i>, <i>Pseudocercospora</i>, <i>Pteridopassalora, Zymoseptoria</i>, and one genus of oomycetes, <i>Phytophthora</i>. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names. <b>Taxonomic novelties: New genera:</b> <i>Heterophaeomoniella</i> L. Mostert, C.F.J. Spies, Halleen & Gramaje, <i>Pteridopassalora</i> C. Nakash. & Crous; <b>New species:</b> <i>Ascochyta flava</i> Qian Chen & L. Cai, <i>Cadophora domestica</i> L. Mostert, R. van der Merwe, Halleen & Gramaje, <i>Cadophora rotunda</i> L. Mostert, R. van der Merwe, Halleen & Gramaje, <i>Cadophora vinacea</i> J.R. Úrbez-Torres, D.T. O'Gorman & Gramaje, <i>Cadophora vivarii</i> L. Mostert, Havenga, Halleen & Gramaje, <i>Celoporthe foliorum</i> H. Suzuki, Marinc. & M.J. Wingf., <i>Cercospora alyssopsidis</i> M. Bakhshi, Zare & Crous, <i>Dendrostoma elaeocarpi</i> C.M. Tian & Q. Yang, <i>Didymella chlamydospora</i> Qian Chen & L. Cai, <i>Didymella gei</i> Qian Chen & L. Cai, <i>Didymella ligulariae</i> Qian Chen & L. Cai, <i>Didymella qilianensis</i> Qian Chen & L. Cai, <i>Didymella uniseptata</i> Qian Chen & L. Cai, <i>Endothia cerciana</i> W. Wang. & S.F. Chen, <i>Leptosphaerulina miscanthi</i> Qian Chen & L. Cai, <i>Nigrospora covidalis</i> M. Raza, Qian Chen & L. Cai, <i>Nigrospora globospora</i> M. Raza, Qian Chen & L. Cai, <i>Nigrospora philosophiae-doctoris</i> M. Raza, Qian Chen & L. Cai, <i>Phytophthora transitoria</i> I. Milenković, T. Májek & T. Jung, <i>Phytophthora panamensis</i> T. Jung, Y. Balci, K. Broders & I. Milenković, <i>Phytophthora variabilis</i> T. Jung, M. Horta Jung & I. Milenković, <i>Pseudocercospora delonicicola</i> C. Nakash., L. Suhaizan & I. Nurul Faziha, <i>Pseudocercospora farfugii</i> C. Nakash., I. Araki, & Ai Ito, <i>Pseudocercospora hardenbergiae</i> Crous & C. Nakash., <i>Pseudocercospora kenyirana</i> C. Nakash., L. Suhaizan & I. Nurul Faziha, <i>Pseudocercospora perrottetiae</i> Crous, C. Nakash. & C.Y. Chen, <i>Pseudocercospora platyceriicola</i> C. Nakash., Y. Hatt, L. Suhaizan & I. Nurul Faziha, <i>Pseudocercospora stemonicola</i> C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, <i>Pseudocercospora terengganuensis</i> 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}
Pub Date : 2022-07-01Epub Date: 2022-04-29DOI: 10.3114/sim.2022.101.04
W Kuephadungphan, B Petcharad, K Tasanathai, D Thanakitpipattana, N Kobmoo, A Khonsanit, R A Samson, J J Luangsa-Ard
Over 80 species of hypocrealean fungi are reported as pathogens of spiders and harvestmen. Among these fungi, the genus Gibellula is highly regarded as a specialised spider-killer that has never been reported to infect other arthropods. While more than 20 species of Gibellula 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 Gibellula 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 Gibellula-infected spider hosts identified Oxyopidae, Uloboridae and, for the first time, the ant-mimicking genus Myrmarachne. Taxonomic novelties: New species:Gibellula brevistipitata Kuephadungphan, Tasanathai & Luangsa-ard, G. longicaudata Tasanathai, Kuephadungphan & Luangsa-ard, G. longispora Kuephadungphan & Luangsa-ard, G. nigelii Kuephadungphan, Tasanathai & Luangsa-ard, G. parvula Kuephadungphan, Tasanathai & Luangsa-ard, G. pilosa Kuephadungphan, Tasanathai & Luangsa-ard, G. solita Kuephadungphan, Tasanathai & Luangsa-ard, G. trimorpha Tasanathai, Khonsanit, Kuephadungphan & Luangsa-ard. Citation: 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, Gibellula (Hypocreales, Cordycipitaceae) in Thailand. Studies in Mycology101: 245-286. doi: 10.3114/sim.2022.101.04.
{"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}
Pub Date : 2022-07-01Epub Date: 2022-01-11DOI: 10.3114/sim.2022.101.01
F Liu, Z Y Ma, L W Hou, Y Z Diao, W P Wu, U Damm, S Song, L Cai
<p><p>The genus <i>Colletotrichum</i> includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated <i>Colletotrichum</i> species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 <i>Colletotrichum</i> 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 <i>Colletotrichum</i>, comprising 16 species complexes (including a newly introduced <i>C. bambusicola</i> 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. <i>Colletotrichum siamense</i>, <i>C. karsti</i>, <i>C. fructicola</i>, <i>C. truncatum</i>, <i>C. fioriniae</i>, and <i>C. gloeosporioides</i> 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 <i>Colletotrichum</i> 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 <i>Colletotrichum</i> 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 <i>Colletotrichum</i> diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus. <b>Taxonomic novelties: New species:</b> <i>Colletotrichum arecacearum</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum bicoloratum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum bromeliacearum</i> F. Liu & L. Cai, <i>Colletotrichum buxi</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum chamaedoreae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum crousii</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum danxiashanense</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum diversisporum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum diversum</i> F. Liu & L. Cai, <i>Colletotrichum dolichoconidiophori</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum iris</i> F. Liu & L. Cai, <i>Colletotrichum monsterae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum multiseptatum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum nageiae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotr
炭疽菌属包括重要的植物病原体、内生菌、腐殖菌和人类病原体。尽管多相方法促进了炭疽菌的物种鉴定，但对整体物种多样性和寄主分布的认识在很大程度上是不完整的。为了解决这一问题，我们从中国87个地点的248属322种植物或空气和土壤样本中分离出952株炭疽菌，以及来自沙特阿拉伯、泰国、土耳其和英国的56株炭疽菌。根据形态特征和多位点系统发育分析，鉴定菌株归属于107种，其中新种30种，中国新记录18种。提供了目前最全面的炭疽菌(Colletotrichum)主干树，包括16个种复合体(包括一个新引进的竹节菌(C. bambusicola)种复合体)和15个单种。在此基础上，该属已知有分子资料的种有280种，其中中国已报道的种有139种，占总数的49.6%。炭疽菌(Colletotrichum siamense)、karsti、C. fructicola、C. truncatum、C. fioriniae和C. gloeosporioides是中国检出最多的种，也是宿主范围最广的种。相比之下，目前在中国发现的与单一植物种或属有关的物种只有76种。迄今为止，有33种炭疽菌被报道为内生菌。此外，我们生成并组装了30个新物种和另外18个已知物种的全基因组序列。基于1 893个单拷贝同源基因，生成了包含94个炭疽病种的最全面的基因组树，除4个节点外，其余节点均为100% bootstrap支持。总的来说，本研究代表了迄今为止最全面的炭疽菌多样性和寄主发生的调查，极大地提高了我们对该属的多样性和系统发育关系的认识。分类学上的新发现:新种;炭疽菌arecacearum f . Liu Z.Y.马& l . Cai刺盘孢属bicoloratum f . Liu W.P.吴& l . Cai刺盘孢属bromeliacearum f·刘& l . Cai刺盘孢属buxi f . Liu W.P.吴& l . Cai刺盘孢属chamaedoreae f . Liu W.P.吴& l . Cai刺盘孢属crousii f . Liu Z.Y.马& l . Cai刺盘孢属danxiashanense f . Liu W.P.吴& l . Cai刺盘孢属diversisporum f . Liu W.P.吴& l . Cai刺盘孢属diversum f·刘& l . Cai刺盘孢属dolichoconidiophori f·刘,虹膜W.P.吴& l . Cai炭疽菌f·刘& l . Cai刺盘孢属monsterae f . Liu W.P.吴& l . Cai刺盘孢属multiseptatum f . Liu W.P.吴& l . Cai刺盘孢属nageiae f . Liu W.P.吴& l . Cai炭疽菌倒卵球形的f·刘& l . Cai刺盘孢属parabambusicola f . Liu W.P.吴& l . Cai刺盘孢属paraendophytum f . Liu W.P.吴& l . Cai刺盘孢属reniforme f . Liu Z.Y.马& l . Cai刺盘孢属schimae f . Liu W.P.吴& l .蔡炭疽菌shivasii f·刘& l . Cai刺盘孢属sinuatum f . Liu W.P.吴& l . Cai刺盘孢属subacidae f . Liu Z.Y.马& l . Cai刺盘孢属subsalicis f·刘& l . Cai刺盘孢属subvariabile f . Liu W.P.吴& l . Cai刺盘孢属syngoniicola f . Liu Z.Y.马& l . Cai刺盘孢属telosmae f . Liu W.P.吴& l . Cai刺盘孢属tibetense f·刘& l . Cai刺盘孢属variabile f . Liu W.P.吴& l . Cai刺盘孢属zhaoqingense f·刘& l .蔡刘峰，吴伟平，蔡磊。引用本文:刘峰，马志勇，侯立文，刁玉柱，吴文武，damu，宋松，蔡玲(2022)。炭疽菌的物种多样性更新及其系统基因组学综述。真菌学研究101:1-56。doi: 10.3114 / sim.2022.101.01。
{"title":"Updating species diversity of <i>Colletotrichum</i>, with a phylogenomic overview.","authors":"F Liu, Z Y Ma, L W Hou, Y Z Diao, W P Wu, U Damm, S Song, L Cai","doi":"10.3114/sim.2022.101.01","DOIUrl":"https://doi.org/10.3114/sim.2022.101.01","url":null,"abstract":"<p><p>The genus <i>Colletotrichum</i> includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated <i>Colletotrichum</i> species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 <i>Colletotrichum</i> 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 <i>Colletotrichum</i>, comprising 16 species complexes (including a newly introduced <i>C. bambusicola</i> 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. <i>Colletotrichum siamense</i>, <i>C. karsti</i>, <i>C. fructicola</i>, <i>C. truncatum</i>, <i>C. fioriniae</i>, and <i>C. gloeosporioides</i> 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 <i>Colletotrichum</i> 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 <i>Colletotrichum</i> 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 <i>Colletotrichum</i> diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus. <b>Taxonomic novelties: New species:</b> <i>Colletotrichum arecacearum</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum bicoloratum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum bromeliacearum</i> F. Liu & L. Cai, <i>Colletotrichum buxi</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum chamaedoreae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum crousii</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum danxiashanense</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum diversisporum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum diversum</i> F. Liu & L. Cai, <i>Colletotrichum dolichoconidiophori</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum iris</i> F. Liu & L. Cai, <i>Colletotrichum monsterae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum multiseptatum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum nageiae</i> F. Liu, W.P. Wu & L. Cai, <i>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}
Pub Date : 2022-07-01Epub Date: 2022-03-30DOI: 10.3114/sim.2022.101.02
Z W de Beer, M Procter, M J Wingfield, S Marincowitz, T A Duong
<p><p>The <i>Ophiostomatales</i> 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 <i>Ophiostomatales</i> 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 <i>Ophiostomatales</i>. 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, <i>i.e.</i> <i>Aureovirgo, Ceratocystiopsis, Esteya, Fragosphaeria, Graphilbum, Hawksworthiomyces, Ophiostoma, Raffaelea</i> and <i>Sporothrix</i>. The two most recently described genera, <i>Chrysosphaeria</i> and <i>Intubia</i>, 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 <i>Ophiostomatales</i>. In addition to the currently accepted genera in the <i>Ophiostomatales</i>, well-supported lineages emerged that were distinct from those genera. These are described as novel genera. Two lineages included the type species of <i>Grosmannia</i> and <i>Dryadomyces</i> and these genera are thus reinstated and their circumscriptions redefined. The descriptions of all genera in the <i>Ophiostomatales</i> 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 <i>Sporothrix</i>. The placement of <i>Afroraffaelea</i> could not be confirmed using the available data and the genus has been treated as <i>incertae sedis</i> in the <i>Ophiostomatales</i>. <i>Paleoambrosia</i> was not included in this study, due to the absence of living material available for this monotypic fossil genus. Overall, this study has pro
{"title":"Generic boundaries in the <i>Ophiostomatales</i> reconsidered and revised.","authors":"Z W de Beer, M Procter, M J Wingfield, S Marincowitz, T A Duong","doi":"10.3114/sim.2022.101.02","DOIUrl":"https://doi.org/10.3114/sim.2022.101.02","url":null,"abstract":"<p><p>The <i>Ophiostomatales</i> 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 <i>Ophiostomatales</i> 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 <i>Ophiostomatales</i>. 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, <i>i.e.</i> <i>Aureovirgo, Ceratocystiopsis, Esteya, Fragosphaeria, Graphilbum, Hawksworthiomyces, Ophiostoma, Raffaelea</i> and <i>Sporothrix</i>. The two most recently described genera, <i>Chrysosphaeria</i> and <i>Intubia</i>, 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 <i>Ophiostomatales</i>. In addition to the currently accepted genera in the <i>Ophiostomatales</i>, well-supported lineages emerged that were distinct from those genera. These are described as novel genera. Two lineages included the type species of <i>Grosmannia</i> and <i>Dryadomyces</i> and these genera are thus reinstated and their circumscriptions redefined. The descriptions of all genera in the <i>Ophiostomatales</i> 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 <i>Sporothrix</i>. The placement of <i>Afroraffaelea</i> could not be confirmed using the available data and the genus has been treated as <i>incertae sedis</i> in the <i>Ophiostomatales</i>. <i>Paleoambrosia</i> 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}
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