F Liu, Z Y Ma, L W Hou, Y Z Diao, W P Wu, U Damm, S Song, L Cai
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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>Colletotrichum obovoides</i> F. Liu & L. Cai, <i>Colletotrichum parabambusicola</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum paraendophytum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum reniforme</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum schimae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum shivasii</i> F. Liu & L. Cai, <i>Colletotrichum sinuatum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum subacidae</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum subsalicis</i> F. Liu & L. Cai, <i>Colletotrichum subvariabile</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum syngoniicola</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum telosmae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum tibetense</i> F. Liu & L. Cai, <i>Colletotrichum variabile</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum zhaoqingense</i> F. Liu & L. Cai, <i>Colletotrichum zhejiangense</i> F. Liu, W.P. Wu & L. Cai. <b>Citation:</b> Liu F, Ma ZY, Hou LW, Diao YZ, Wu WP, Damm U, Song S, Cai L (2022). Updating species diversity of <i>Colletotrichum</i>, with a phylogenomic overview. <i>Studies in Mycology</i> <b>101</b>: 1-56. doi: 10.3114/sim.2022.101.01.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":null,"pages":null},"PeriodicalIF":14.1000,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365046/pdf/","citationCount":"42","resultStr":"{\"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\":null,\"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>Colletotrichum obovoides</i> F. Liu & L. Cai, <i>Colletotrichum parabambusicola</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum paraendophytum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum reniforme</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum schimae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum shivasii</i> F. Liu & L. Cai, <i>Colletotrichum sinuatum</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum subacidae</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum subsalicis</i> F. Liu & L. Cai, <i>Colletotrichum subvariabile</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum syngoniicola</i> F. Liu, Z.Y. Ma & L. Cai, <i>Colletotrichum telosmae</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum tibetense</i> F. Liu & L. Cai, <i>Colletotrichum variabile</i> F. Liu, W.P. Wu & L. Cai, <i>Colletotrichum zhaoqingense</i> F. Liu & L. 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引用次数: 42
摘要
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。
Updating species diversity of Colletotrichum, with a phylogenomic overview.
The genus Colletotrichum includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated Colletotrichum species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 Colletotrichum 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 Colletotrichum, comprising 16 species complexes (including a newly introduced C. bambusicola 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. Colletotrichum siamense, C. karsti, C. fructicola, C. truncatum, C. fioriniae, and C. gloeosporioides 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 Colletotrichum 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 Colletotrichum 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 Colletotrichum diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus. Taxonomic novelties: New species:Colletotrichum arecacearum F. Liu, Z.Y. Ma & L. Cai, Colletotrichum bicoloratum F. Liu, W.P. Wu & L. Cai, Colletotrichum bromeliacearum F. Liu & L. Cai, Colletotrichum buxi F. Liu, W.P. Wu & L. Cai, Colletotrichum chamaedoreae F. Liu, W.P. Wu & L. Cai, Colletotrichum crousii F. Liu, Z.Y. Ma & L. Cai, Colletotrichum danxiashanense F. Liu, W.P. Wu & L. Cai, Colletotrichum diversisporum F. Liu, W.P. Wu & L. Cai, Colletotrichum diversum F. Liu & L. Cai, Colletotrichum dolichoconidiophori F. Liu, W.P. Wu & L. Cai, Colletotrichum iris F. Liu & L. Cai, Colletotrichum monsterae F. Liu, W.P. Wu & L. Cai, Colletotrichum multiseptatum F. Liu, W.P. Wu & L. Cai, Colletotrichum nageiae F. Liu, W.P. Wu & L. Cai, Colletotrichum obovoides F. Liu & L. Cai, Colletotrichum parabambusicola F. Liu, W.P. Wu & L. Cai, Colletotrichum paraendophytum F. Liu, W.P. Wu & L. Cai, Colletotrichum reniforme F. Liu, Z.Y. Ma & L. Cai, Colletotrichum schimae F. Liu, W.P. Wu & L. Cai, Colletotrichum shivasii F. Liu & L. Cai, Colletotrichum sinuatum F. Liu, W.P. Wu & L. Cai, Colletotrichum subacidae F. Liu, Z.Y. Ma & L. Cai, Colletotrichum subsalicis F. Liu & L. Cai, Colletotrichum subvariabile F. Liu, W.P. Wu & L. Cai, Colletotrichum syngoniicola F. Liu, Z.Y. Ma & L. Cai, Colletotrichum telosmae F. Liu, W.P. Wu & L. Cai, Colletotrichum tibetense F. Liu & L. Cai, Colletotrichum variabile F. Liu, W.P. Wu & L. Cai, Colletotrichum zhaoqingense F. Liu & L. Cai, Colletotrichum zhejiangense F. Liu, W.P. Wu & L. Cai. Citation: Liu F, Ma ZY, Hou LW, Diao YZ, Wu WP, Damm U, Song S, Cai L (2022). Updating species diversity of Colletotrichum, with a phylogenomic overview. Studies in Mycology101: 1-56. doi: 10.3114/sim.2022.101.01.
期刊介绍:
The international journal Studies in Mycology focuses on advancing the understanding of filamentous fungi, yeasts, and various aspects of mycology. It publishes comprehensive systematic monographs as well as topical issues covering a wide range of subjects including biotechnology, ecology, molecular biology, pathology, and systematics. This Open-Access journal offers unrestricted access to its content.
Each issue of Studies in Mycology consists of around 5 to 6 papers, either in the form of monographs or special focused topics. Unlike traditional length restrictions, the journal encourages submissions of manuscripts with a minimum of 50 A4 pages in print. This ensures a thorough exploration and presentation of the research findings, maximizing the depth of the published work.