Whole genome and transcriptome analysis of Colletotrichum falcatum – a prelude on deciphering specific adaptation as intriguing stalk pathogen

Abstract

The Colletotrichum falcatum pathotype CF06 (isolated from sugarcane cv CoC 671; MTCC accession number-12142) was sequenced on using HiSeq 2000 platform (Genotypic solutions, Bengaluru) and assembled into contigs and scaffolds based on pair-end library using Velvet assembler and contig extension/ scaffolding done by SSPACE. The genome of C. falcatum is 48.2 MB with predicted 12,270 genes at 150x coverage (Bio Project ID-272959, Accession number - PRJNA272959). The sequenced genome of C. falcatum was comparable in size to the recently reported Colletotrichum spp . The arsenal of C. falcatum genes involved in hemibiotrophic lifestyle is found to be similar with C. graminicola and C. sublineola infecting related hosts maize and sorghum, respectively. The genome of C. falcatum revealed presence of plant cell wall degrading enzymes (PCW), candidate secretory effectors (CSEPs), transposable elements, primary & secondary metabolites, membrane transporters, signaling molecules, CAZy, mating proteins involved in development and sclerotic management proteins. Further, sequencing of expressed transcripts of the fungal pathogen using Illumina Hi-Seq technology generated a total of 53,410,513 reads (50 bp read length) specific to C. falcatum. The sequences were assembled into 24,732 transcripts representing 23,136 predicted coding regions. Interestingly, large number of transcripts encoding biotrophy-necrotrophy transition and membrane transporters were identified and gene enrichment analysis revealed that the number of transporters encoded by C. falcatum is significantly more as compared to other Colletotrichum species. Exploring genome and transcriptome pave a way in understanding the biology of the red rot pathogen and this has identified several unique putative genes/functions required for its pathogenesis in sugarcane. Further, this work lays the foundation for facilitating future research towards understanding this intriguing host-pathogen interaction.