Deep sequencing analysis of virus-derived small RNAs in tomato plants infected by Tomato yellow leaf curl Sardinia virus

Tomato yellow leaf curl Sardinia virus (TYLCSV) is a Begomovirus with a genome consisting of a circular single-stranded DNA molecule ca. 2800 bases in length. Its bidirectional promoter drives the generation of viral RNA transcripts coding for viral proteins required for its entire life cycle in the host plant. The RNA silencing machinery recognises the viral transcripts as foreign RNAs, thus leading on to the production of viral small interfering RNAs (v-siRNAs), likely responsible for v-siRNA-mediated antiviral defense. A cDNA library of small RNAs was generated from tissues of TYLCSV-infected tomato plants and sequenced on Solexa/Illumina sequencing platform. The subset of v-siRNAs was therefore identified; the major size classes of TYLCSV-derived siRNAs were 21 and 22 nt species spanning the entire viral genome but being discontinuously distributed throughout it. The most abundant v-siRNAs are from CP and C4 genes, whereas those from the intergenic region are poorly represented. Moreover, the majority of v-siRNAs are of sense polarity suggesting that they are from folded single-stranded viral transcript, similarly to what observed in the case of other v-siRNAs from positive stranded RNA plant viruses. The possible mechanism/s of v-siRNA biogenesis and their role in antiviral plant response will be also discussed.