Spore type-specific gene expression profiles underlying development and leaf infection processes of Colletotrichum graminicola

Colletotrichum graminicola causes significant losses of the staple crop maize worldwide. The fungus produces two distinct asexual spore types, oval and falcate conidia, which show unique processes in development and plant interaction. Based on genome resequencing of our laboratory strain (CgM2/ M1.001), we investigated the gene expression profiles of oval and falcate conidia during development and the establishment of the biotrophic phase after leaf penetration using RNA-seq. Our results reveal specific gene expression profiles between the two spore types, indicating fundamental differences in their developmental programs that reflect different modes of infection. We identified spore type-specific expression patterns for genes encoding transcription factors, conserved fungal developmental genes, transporters, genes of secondary metabolite clusters, and pathogenicity-related functions, including effectors and carbohydrate-active enzymes (CAZymes). Our study shows that despite of the identical genomic basis, oval and falcate conidia have their own identity, and retain it in the process of germination, plant penetration, and biotrophy. Taken together, these results provide new insights into the molecular mechanisms underlying the infection process and have significant implications for understanding the biology of C. graminicola and its interaction with the plant host.