Virus-derived small RNAs in tomato plants infected by Tomato yellow leaf curl Sardinia virus analysed by deep sequencing

Background: The begomovirus Tomato yellow leaf curl Sardinia virus (TYLCSV) induces a devastating disease of tomato crops in the Mediterranean region. TYLCSV has a 2.7 kb circular single-stranded DNA genome that includes a bidirectional promoter driving the synthesis of viral RNA transcripts. These are recognised by the plant RNA silencing machinery as foreign RNAs that generate viral small interfering RNAs (v-siRNAs). Methods: A cDNA library of small RNAs was obtained from TYLCSV-infected tomato plants and sequenced on Solexa/Illumina platform. The subset of v-siRNAs was identified and characterized. Results: TYLCSV-derived siRNAs, mainly of 21-22 nt, spanned the entire viral genome but were discontinuously distributed throughout it. Viral-siRNAs from the non-coding region were poorly represented; the most abundant v-siRNAs were from the coat protein and the Rep/C4 genes and were mainly of sense polarity. The major hot spots were experimentally validated by reverse oligo dot blot analysis. Conclusions: The first high-resolution v-siRNA map for TYLCSV is reported. The mechanism/s of v-siRNA biogenesis and their role in antiviral plant response are discussed.