Differential expression profiling of Ustilaginoidea virens in resistant and susceptible rice varieties during early infection

To understand pathogenicity and in planta transcriptional reprogramming, expression profiles of U. virens during infection of the resistant and susceptible cultivars were analyzed using RNA-seq data. Predicted host-pathogen interaction database (PHI-base) genes that are probably involved in host-pathogen interactions were found to be significantly enriched in fungal differential expressed genes from both rice genotypes, indicating their potential roles in pathogenicity of U.virens. Our results also indicate that genes for secreted proteins and secondary metabolism are highly enriched in the transcriptome during early infection of susceptible cultivars. GO enrichment analysis suggest that bilogical processes required for successful infection of U. virens are greatly suppressed in the resistant cultivars. Overall design: Oryza sativa L. spp. indica cultivars IR28 (resistant) and LYP9 (susceptible) were used in our experiments. Rice panicles were inoculated with a mixture of conidial and hyphal fragments of U. virens P1 strain. Total RNA was isolated from in vitro cultures and from inoculated rice panicles using RNApure RNA isolation kit according to the manufacturer’s instruction. Total RNA from three biological replicates at each time point (6 h.p.i., 24 h.p.i. and 48 h.p.i.) were combined and used for library construction. Each library had an insert size of ~200 bp. The reads of 49 bp (for in planta expression profiling) or 100 bp (for transcriptome analysis of in vitro cultures) sequences were generated via Illumina HiSeq2000 at BGI.