Genome Evolution of Colletotrichum

Genome evolution of Colletotrichum

Fang Liu*, Ziying Ma and Lei Cai*

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
*Email: Lei Cai:; Fang Liu:,

Colletotrichum is one of the most devastating global fungal phytopathogens, well-known for their wide host ranges and pathogenicity. However, despite the diversity and prevalence of Colletotrichum, there is limited understanding on the genome-wide evolutionary mechanisms, adaptations and host specificity. We thus recently generated de novo sequence assemblies for 84 Colletotrichum species, and found that phylogenetic relationships were significantly correlated with genome size. Species with larger genomes were mainly due to the expansion of repetitive sequences, especially long terminal repeat retrotransposons and some unclassified repeats. The analysis results of molecular clock and ancestral state reconstruction showed that the ancestral speciation time of Colletotrichum was about 47 million years ago, and the change of its host range was jointly affected by climate and human activities. In particular in the C. gloeosporioides species complex (CGSC), we found that human activities have influenced the dispersal and domestication of plants, and in turn the evolution of phytopathogenic fungi. During this time, an intra-chromosomal inversion may have driven the divergence of a major clade (Kahawae clade) from its ancestor in CGSC. In addition, a rapid speciation event of C. kahawae may have occurred after the emergence of its host plant and the extensive chromosomal rearrangements mediated by repetitive sequences resulted in highly dynamic lineage-specific genomic regions which enriched for CYP450s and secondary metabolite gene clusters. The results provided new insights into the evolution of these plant pathogenic fungi and their interaction with host plants.