Interaction map of Tomato spotted wilt virus-specific small RNAs and the tomato transcriptome

Abstract

Tomato spotted wilt virus (TSWV; Tospovirus:Bunyaviridae) is one of the most prolific and economically important viruses of field and horticultural crops. In the plant-virus interactions, virus-derived siRNAs (vsiRNAs) are the result of activity of host-mediated silencing mechanism. We recently obtained the TSWV-specific small RNA profiles from virus-infected tomato. A subset of siRNAs derived from the TSWV genome hotspots was analyzed in silico for their propensity to down regulate tomato transcriptome. vsiRNAs were found to interact with a gamut of host genes involved in basal cellular activities such as nucleic acid metabolism, ribosomal turnover, translational factors, cytoskeletal proteins, phenylpropanoid biosynthesis, glycosyl transferases, peptidases, hormonal signalling, protein kinases, intercellular transporter genes, and stress-related proteins. Notably, vsiRNAs derived from the TSWV NSs gene binds with transcripts generally associated with stress signalling, whereas siRNAs from NSm were predominantly found to bind the transcripts involved in abiotic stress responses such as dehydration responsive protein, ion exchange transporters, and low temperature and salt responsive proteins. The predicted interactome scenario when validated through gene expression studies using RNAseq could provide a detailed picture on the molecular mechanism underlying the tospovirus-plant interactions.