Taxonomy and biodiversity of Colletotrichum

Abstract

Colletotrichum includes several important plant pathogens causing anthracnose diseases of a wide variety of woody and herbaceous host plants. However, misidentifications of Colletotrichum species are frequent due to few distinctive morphological characters and a general misunderstanding of their host-specific nature. Although we are able to generate more objective data relating to the taxonomic treatment of this genus since the advent of DNA sequence technology, there are still many issues in studying this genus that need to be resolved. For example: 1) many old Colletotrichum names lack type specimens and cultures that are suitable for molecular analysis, which tend to hinder the reconstruction of a natural classification system; 2) many species names are still applied in their broad sense for anthracnose pathogens of commercially important crops and fruits; 3) novel analytical methods need to be considered for the taxonomic study of Colletotrichum to overcome the defect of PSR and GCPSR on species delimitation.A detailed study of 349 Colletotrichum isolates was completed incorporating morphological characterisation and DNA sequence data from 11 loci (ACT, ApMat, Apn25L, CAL, CHS-1, GAPDH, GS, HIS3, ITS, MAT1-2-1, TUB2). To preserve the current application of names in Colletotrichum, the epi- or neotypes for three important Colletotrichum species were designated, i.e., C. lindemuthianum, C. nigrum and C. camelliae. A previously unknown species complex with larger conidia than that of other species in Colletotrichum, i.e. the C. gigasporum species complex, was proposed based on morphology and phylogeny of five loci, including one species (C. gigasporum) that was once reported from a human patient in Brazil. Nine new species were treated in this thesis. In addition to these novel discoveries, the high biodiversity of Colletotrichum species associated with Camellia and Proteaceae of commercial importance was unraveled.In this study, the coalescent methods of General Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP) and Bayesian Phylogenetics and Phylogeography (BP&P) were newlyintroduced into the taxonomic study of Colletotrichum to overcome the defect of PSR and GCPSR on species delimitation, which could avoid arbitrary cut-offs and over-supporting of poorly resolved clades. Combined with the analyses of genetic recombination, mating test, and the comparison of ecological and morphological characters, we rejected the null hypothesis that C. siamense is a species complex and demonstrated the significance of a large sampling size coupled with a polyphasic approach to species delimitation.