Multi-approach analysis of the diversity in Colletotrichum cliviae sensu lato

Abstract

Colletotrichum cliviae is a fungal species reported both as pathogen and endophyte with broad geographical distribution. Some purported isolates of this species have been assigned to different taxa, including Colletotrichum aracearum, Colletotrichum orchidearum and Colletotrichum. sichuanensis, for which a preliminary analysis of extensive multilocus (ACT, GAPDH, ITS, TUB2) data in this study revealed high sequence similarity with C. cliviae. We further reassessed the species delineation by using the coalescent method of the generalized mixed Yule-coalescent (GMYC) and Poisson Tree Processes (PTP). Single and multilocus gene trees strongly supported a C. cliviae s. lat. clade including the four species. This clade unfolded eight subclades grouped into three distinct lineages, but no monophyly of any of the four species. GMYC and PTP analyses confidently supported the evolutionary independence of these lineages. C. sichuanensis and C. cliviae, except one isolate, formed the largest lineage. The second lineage was made up of isolates named C. aracearum and some of C. orchidearum sharing the haplotype and the third lineage accommodated two isolates named C. cliviae and C. orchidearum. This finding suggests the synonymization of C. sichuanensis with C. cliviae whereas the taxonomic status of C. aracearum and C. orchidearum still needs clarification. This study lays great stress upon the use of comprehensive data for sequence-based characterisation of species in the C. cliviae s. lat. It also presents the first report of C. cliviae in tropical Africa and on citrus host.

The Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes

“…In a study of Douanla-Meli et al. (2018) , C. plurivorum ( as C. sichuanensis ) was regarded as a synonym of C. cliviicola (as C. cliviae ), although both species formed well supported clades in the phylogeny based on a multilocus data set and there was no indication of disconcordance between the gene trees.…”

“…and Saccharum sp. in India ( Sharma et al., 2013b , Chowdappa et al., 2014 ), Myrianthus arboreus in Cameroon, Citrus limon in Vietnam ( Douanla-Meli et al. 2018 ) and as an endophyte on Camellia sinensis and Mangifera indica in Brazil and China, respectively ( Vieira et al., 2014 , Liu et al., 2015 ).…”

“…Based on this study, C. cliviicola is a distinct species. The C. cliviae clade in Douanla-Meli et al. (2018) also included strains from an undetermined ornamental plant in India that could also be Clivia .…”

Colletotrichum species associated with cassava anthracnose in China

“…Colletotrichum plurivorum was first described as C. sichuanensis from Capsicum annuum in Sichuan Province, China (Liu et al, ). In a study by Douanla‐Meli, Unger, and Langer (), C. sichuanensis was regarded as a synonym of C. cliviicola (as C. cliviae ), while was found to in a study by Damm et al (), C. cliviicola and C. plurivorum were once again regarded as distinct species. C. plurivorum was found to form a sexual morph, an asexual morph, or both morphs in culture (Damm et al, ).…”

“…based on comparisons of DNA sequence were also revealed to be C. plurivorum. This species is known to have a large host range of more than 20 species (Damm et al, 2018;Douanla-Meli et al, 2018). Colletotrichum karstii is known as a pathogen or endophyte of many species belonging to the Orchidaceae in China (Yang, et al, 2011), and its host range was recently extended to more plants (Damm, Cannon, Woudenberg, Johnston, et al, 2012;Guarnaccia, Groenewald, Polizzi, & Crous, 2017;Liu et al, 2015;Sharma, Pinnaka, & Shenoy, 2013).…”