Genome-wide identification of host and viral transcripts targeted by viral siRNAs in Vitis vinifera.

In plants, RNA silencing is a surveillance mechanism against invading viruses. It involves the production of virus-derived small interfering RNAs (vsiRNAs), which guide the RNA-induced silencing complex (RISC) to inactivate viruses. Moreover, vsiRNAs may promote silencing of host mRNAs in a sequence-specific manner. To date, little is known about the efficiency of these vsiRNAs in guiding effector complexes to cleave target viral sequences or host transcripts. We have identified vsiRNAs derived from two grapevine-infecting viruses (Grapevine fleck virus and Rupestris stem pitting-associated virus) using the Illumina platform for deep sequencing. To better understand the role of vsiRNAs, a degradome analysis of viral RNA 5'-ends was analysed; it can identify the remnants of cleaved host transcripts and viral RNA targets. By integrating vsiRNA and degradome data, we have identified ca. 50 host transcripts targeted by vsiRNAs including. Among them, several encode putative proteins involved in ribosome biogenesis and in biotic and abiotic stresses and in other cellular pathways. Moreover, we have identified vsiRNAs which explains cleavage sites in viral genomes. A consistent fraction of vsiRNAs did not account for cleavage sites, suggesting that relatively few vsiRNAs are involved in the antiviral response. Aspects of vsiRNA-driven RNA targeting are discussed