Comparative Genomics and Transcriptome Analysis of Two Colletotrichum scovillei Strains Revealed Genes Involved in Pathogenicity on Pepper (Capsicum annuum L.)

Colletotrichum scovillei causes anthracnose in chilli pepper worldwide, which is one of the most serious diseases affecting the production of pepper fruits. Although there are several studies on the Colletotrichum disease genes identified, there are still gaps in the understanding of the pathogenic genes and pathogenic mechanisms of Colletotrichum. In this study, two Colletotrichum strains, C. scovillei (Colletotrichum scovillei) C1 and C. scovillei CD showed different virulence against chill pepper, with C. scovillei C1 having a marked virulence defect compared to C. scovillei CD. To explore the genetic variation between the two strains, comparative genomic and transcriptome analyses were conducted to reveal the functional genes associated with the virulence. At the genome level, C. scovillei C1 was found to have a number of structural variation (SVs), insertion and deletion (InDels) and single nucleotide polymorphisms (SNPs) compared with C. scovillei CD. Analysis of DEGs (differentially expressed genes) between C. scovillei C1 and C. scovillei CD at the transcriptome level revealed 106 DEGs, including three upregulated effectors in C. scovillei CD, which might be the reasons for the high virulence of C. scovillei CD. In summary, our study revealed the genomic and transcriptomic mechanism involved in C. scovillei virulence in pepper, which contributes to the understanding of pepper anthracnose pathogenicity.