TSWV-infected S. lycopersicum and N. benthamiana Small RNA sequencing

Tomato spotted wilt virus (TSWV), genus Tospovirus, family Bunyaviridae has a segmented negative-stranded RNA genome, with two of its gene segments showing ambisense gene arrangement. The virus causes significant economic losses to numerous field and horticultural crops worldwide. There are no reports on the analysis of vsiRNAs produced in host plants following infection by TSWV. TSWV-specific vsiRNAs were characterized by deep sequencing in virus-infected experimental host Nicotiana benthamiana and a commercial, susceptible host tomato (Lycopersicon esculentum). The TSWV-infected tomato sample showed relatively equal distribution of 21, 22 and 24 nt total small RNAs, whereas N. benthamiana sample was dominated by 24 nt small RNAs. The number of TSWV-specific vsiRNA reads detected in tomato was many a magnitude (~ 350:1) higher than those found in N. benthamiana having the same virus titer. The vsiRNA population in both hosts was dominated by 21 and 22 nt species. Maximum vsiRNA reads were obtained for M RNA segment of TSWV while the largest L RNA segment had the least number of vsiRNAs in both hosts. Only the silencing suppressor, NSs, of TSWV recorded higher antisense vsiRNA among all the genes of TSWV. Details of the origin, distribution and abundance of TSWV vsiRNAs could be useful in designing efficient targets for exploiting RNA interference for virus resistance. It also has major implications toward our understanding of the differential processing of vsiRNAs in antiviral defense and viral pathogenicity.