Transcriptome Analysis of Sugarcane Response to the Infection by Sugarcane Steak Mosaic Virus (SCSMV)

Abstract

Sugarcane streak mosaic virus (SCSMV) is one of the pathogens causing sugarcane mosaic disease (SMD). Transcriptome of a susceptible sugarcane cultivar challenged by SCSMV was studied by high-throughput, paired-end RNA sequencing. Overall, we obtained 63,025 unigenes, including 14,384 unigenes measuring more than 1 kb each. We annotated 38,505 unigenes with COG, GO, KEGG, KOG, Pfam, Swiss-Prot and Nr. We screened 4982 differently expressed genes (DEGs) including 3841 annotated DEGs, of which 3791 were up-regulated, and 50 were down-regulated. The expression of DEGs in the three KEGG pathways, unbiquitin proteolytic system, proteasome and translational pathways in endoplasmic reticulum (ER) was investigated in response to stress and unfolded protein response (UPR). Interestingly, the DEGs in the 3 pathways were up-regulated. We tested eight DEGs encoding proteins in response to ER stress and UPR. We found that these genes were up-regulated in sugarcane challenged by SCSMV. This study presented the first report of the sugarcane transcriptome following SCSMV infection. It sheds light on the genetic mechanisms in sugarcane in response to SCSMV infection.