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Open Access Updating species diversity of Colletotrichum, with a phylogenomic overview

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The genus Colletotrichum includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitatedColletotrichum species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952Colletotrichum 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 ofColletotrichum, 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 ofColletotrichum diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus.

Keywords: BACKBONE TREE; FUNGAL SYSTEMATICS; MULTI-LOCUS PHYLOGENY; NEW TAXA; PHYLOGENOMICS; PLANT PATHOGEN; TAXONOMY

Document Type: Research Article

Publication date: March 1, 2022

This article was made available online on January 11, 2022 as a Fast Track article with title: "Updating species diversity of Colletotrichum, with a phylogenomic overview".

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  • Studies in Mycology is an international journal which publishes systematic monographs of filamentous fungi and yeasts, and special topical issues related to all fields of mycology, biotechnology, ecology, molecular biology, pathology and systematics. The journal is Open-Access and contains monographs or topical issues (5–6 papers per issue). There are no restrictions of length, although it is generally expected that manuscripts should be at least 50 A4 pages in print.
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