Comparative genome analysis indicates rapid evolution of pathogenicity genes in Colletotrichum tanaceti

ABSTRACTColletotrichum tanacetiis an emerging foliar fungal pathogen of pyrethrum (Tanacetum cinerariifolium), posing a threat to the global pyrethrum industry. Despite being reported consistently from field surveys in Australia, the molecular basis of pathogenicity ofC. tanacetion pyrethrum is unknown. Herein, the genome ofC. tanaceti(isolate BRIP57314) was assembledde novoand annotated using transcriptomic evidence. The inferred pathogenicity gene suite ofC. tanaceticomprised a large array of genes encoding secreted effectors, proteases, CAZymes and secondary metabolites. Comparative analysis of its CAZyme pathogenicity profiles with those of closely related species suggested thatC. tanacetihad additional hosts to pyrethrum. The genome ofC. tanacetihad a high repeat content and repetitive elements were located significantly closer to genes inferred to influence pathogenicity than other genes. These repeats are likely to have accelerated mutational and transposition rates in the genome, resulting in a rapid evolution of certain CAZyme families in this species. TheC. tanacetigenome consisted of a gene-sparse, A-T rich region facilitating a “two-speed” genome. Pathogenicity genes within this region were likely to have a higher evolutionary rate than the ‘core’ genome. This “two-speed” genome phenomenon in certainColletotrichumspp. was hypothesized to have caused the clustering of species based on the pathogenicity genes, to deviate from taxonomy. With the large repertoire of pathogenicity factors that can potentially evolve rapidly in response to control measures,C. tanacetimay pose a high-risk to global pyrethrum production. Knowledge of the pathogenicity genes will facilitate future research in disease management ofC. tanacetiand otherColletotrichumspp..