Comparative transcriptome analysis of candidate secretory effector proteins from Colletotrichum falcatum infecting sugarcane

Abstract

The ascomycete Colletotrichum falcatum is the causal agent of red rot of sugarcane, infecting stalks which are economically important for extraction of sugar. Since the pathogen is considered as the most destructive disease in many sugarcane growing countries it gained much attention to decipher its lifestyle. In this study, we have sequenced in planta transcriptome of C. falcatum under Illumina Hi-Seq platform and expanded our search towards finding the Small Secretory Proteins (SSPs) expressed during the host-pathogen interactions. Our previous reports from genome and transcriptome of C.falcatum data provided 768 and 884 SSPs were predicted respectively. The in planta secretory proteins were further mapped and localized with the help of bioinformatics pieplines such as TargetP and SignalP with the default parameters resulted in localizing 739 sequences to secretory pathway, 27 as mitochondrion and two contained chloroplast signal peptides. Further, the predicted secretory proteins were grouped into classical and non-classical proteins and these secreted proteins and 56 transmembrane helices were classified using GO, which revealed that signal peptides have a probable role in stabilizing fungal secretory proteins in the host system during pathogenesis. These small secreted proteins were further identified as crucial key pathogenic determinants from in planta transcriptome analysis. The repertoire of C. falcatum effectors prediction from in vitro and in planta transcriptome identified several putative genes which are involved in biotrophy-necrotrophy in functionally diverse patterns and this will facilitate further analysis of stage specific genes, fungal pathogenicity determinants and characterizing the expression of SSPs in in planta.