Transcriptome analysis of host-pathogen interaction between sugarcane and Colletotrichum falcatum by Suppression Subtractive Hybridization and Illumina sequencing

Abstract

A high throughput analyses of interaction between sugarcane and Colletotrichum falcatum, the hemibiotrophic pathogen causing red rot, was made by comparing transcriptomes of compatible and incompatible interactions in a tropical sugarcane cultivar Co7805 exhibiting differential reaction to the pathotypes Cf94012 and Cf87012, respectively. Suppression subtractive hybridization (SSH) combined with Illumina 2000 high throughput sequencing was used to identify the differential transcripts in resistance response library (RRL) and susceptible response library (SRL). After processing and filtering the raw reads from Illumina 2000 high throughput sequencing of subtracted products, we obtained 10,038 and 4,022 high quality transcripts, from RRL and SRL, respectively. Based on the transcripts mapping to KEGG-KASS database, the presence of a CEBiP receptor and the signals ROS, Ca2+, BR, JA and ABA were identified in both the responses. However, MAPK, ET, PI signals and JA amino conjugation were found only in the incompatible interaction and expression of 10 transcripts involved in these pathways was validated using qRT-PCR. Our study concludes that perception of PAMPs occurs in both systems, but downstream signaling through MAPK, ET, PI and JA amino conjugation and activation of R genes occurs only in the incompatible interaction. This is the first detailed transcriptomic analysis of compatible and incompatible interactions in sugarcane with two different C. falcatum pathotypes through SSH and the next generation sequencing (NGS) platform.