Unraveling the Genetic Complexities in Gene Set of Sugarcane Red Rot Pathogen Colletotrichum falcatum Through Transcriptomic Approach

Abstract

The transcriptome-based gene set expression of a unique sugarcane stalk infecting fungal pathogen reveals novels insights in deciphering the class of pathogenicity genes present in Colletotrichum falcatum. This study gains significance in understanding the genetic signature of this pathogen using RNA-Seq technology. A total of 53,410,513 reads (24,732 transcripts) specific to C. falcatum were generated, and 13,320 genes were predicted. Gene ontology distributions have been grouped into three domains as biological (3053), cellular (1601) and molecular functions (3444). KEGG annotations represented pathway biomolecules such as carbohydrates, lipids, nucleotides, amino acids, glycans, cofactors, vitamins, terpenoids and polyketides. The genes for virulence have been classified and grouped into candidate effectors, transition-specific and secondary metabolites, proteases, transporters and peptidases which revealed that C. falcatum transcripts encode a large number of secondary metabolites and membrane transporters. Gene enrichment analysis revealed that the number of transporters encoded by C. falcatum is significantly more as compared to that encoded by several other Colletotrichum spp. Phylogenomics analysis indicated that C. falcatum is closely related to C. graminicola and C. sublineola infecting related host plants, maize and sorghum, respectively. This study provides a comprehensive understanding of C. falcatum pathobiology and has identified many candidate genes/putative functions possibly required for its pathogenesis.