Characterization of viral short-RNAs in Brassica napus and Brassica rapa infected with Cauliflower mosaic virus

Virus infections are accompanied by massive amount of viral (v) short-interfering (si)RNAs, due to the plant antiviral RNA silencing machinery. Recently, virus-activated (va) endogenous siRNAs have been also found associated to viral infections and are believed to play key roles in plant-virus interaction. Cauliflower mosaic virus (CaMV) is one of the important pathogens infecting members of Brassicaceae family with economic impact. Here we describe a functional characterization of CaMV v-siRNAs in either infected turnip (Brassica rapa), a sensitive host to CaMV, or canola (Brassica napus) as semisensitive host. We found that vsiRNA derive from all the viral genome, thus in contrast with what previously observed in the model plant Arabidopsis. Importantly, the vsiRNA distribution did not differ between turnip and canola, thus suggesting the different sensitivity of the two hosts to CaMV infection is not due to the sole production of vsiRNAs. Indeed, here we showed CaMV infections were accompanied by the production of endogenous sRNAs associated to diverse genomic regions, likely CaMV-triggered vasiRNAs. CaMV-triggered vasiRNAs are 21-24 nucleotide in length and are associated to either coding genes or non-coding loci with a 2-to-1 ratio between sense/antisense referred to the orientation of the gene. Also we found some endogenous sRNAs that were produced only in mock-inoculated plants but not in infected types. Notably, most of the coding genes derived vasiRNAs of both CaMV-infected turnip/canola, were from genes involved at different steps of the photosynthesis process. On the other hands, most of non-coding derived vasiRNAs were from 18s rRNA and 28s rRNA.