Small RNA sequencing and assembly: reconstructing viral genomes from defence molecules

RNA silencing constitutes a fundamental antiviral defence mechanism in plants in which host enzymes cut viral RNA into pieces of 20-24 nucleotides. When isolated, sequenced en mass and properly assembled or aligned these virus-derived small RNA (sRNA) sequences can reconstitute genomic sequence information of the viruses being targeted in the plant. This approach is independent of the ability to culture or purify the virus and does not require any specific amplification or enrichment of viral nucleic acids as it automatically enriches for small RNAs of viral origin by tapping into a natural antiviral defence mechanism. Results from the application of this technique to identify novel plant viruses as well as map variability and distribution of viruses will be presented.