Liu F, Ma Z Y, Hou L W, Diao Y Z, Wu W P, Damm U, Song S, Cai L
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Stud Mycol. 2022 Jul;101:1-56. doi: 10.3114/sim.2022.101.01. Epub 2022 Jan 11.
The genus includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 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 , comprising 16 species complexes (including a newly introduced 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. , , , , , and 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 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 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 diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus. F. Liu, Z.Y. Ma & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, Z.Y. Ma & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, Z.Y. Ma & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, Z.Y. Ma & L. Cai, F. Liu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu, Z.Y. Ma & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu & L. Cai, F. Liu, W.P. Wu & L. Cai, F. Liu & L. Cai, F. Liu, W.P. Wu & L. Cai. Liu F, Ma ZY, Hou LW, Diao YZ, Wu WP, Damm U, Song S, Cai L (2022). Updating species diversity of , with a phylogenomic overview. : 1-56. doi: 10.3114/sim.2022.101.01.
该属包括重要的植物病原体、内生菌、腐生菌和人类病原体。尽管多相分类法有助于物种鉴定，但对该属整体物种多样性和宿主分布的了解仍很不完整。为解决这一问题，我们研究了从中国87个地点的248个属的322种植物、空气和土壤样本中分离出的952株菌株，以及来自沙特阿拉伯、泰国、土耳其和英国的56株菌株。基于形态特征和多位点系统发育分析，这些菌株被归为107个物种，包括本文描述的30个新物种和中国的18个新记录。提供了目前最全面的该属主干树，包括16个物种复合体（包括一个新引入的物种复合体）和15个单型物种。基于这些分析，该属有280个有可用分子数据的物种被认可，其中139个在中国有报道，占该属物种的49.6%。在中国，[物种名称1]、[物种名称2]、[物种名称3]、[物种名称4]、[物种名称5]和[物种名称6]是最常检测到的物种，也是宿主范围最广的物种。相比之下，目前发现有76个物种在中国仅与单一植物物种或属相关。迄今为止，有33个物种被专门报道为内生菌。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。由此生成了基于1893个单拷贝直系同源基因的包含94个物种的最全面的基因组树，除四个节点外，所有节点的自展值均为100%。总体而言，这项研究是迄今为止对该属多样性和宿主出现情况最全面的调查，并大大增进了我们对该属多样性和系统发育关系的理解。刘F、马ZY、侯LW、刁YZ、吴WP、达姆U、宋S、蔡L（2022年）。更新[属名]的物种多样性，并进行系统基因组概述。[期刊名]：1 - 56。doi: 10.3114/sim.2022.101.01 。 （注：原文中部分物种名称未给出具体内容，用[物种名称X]表示）
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