Deep sequencing applied to virus analysis ans discovery

Deep sequencing is a powerful technology that provides information on the infectious agents (viruses and viroids) present in plant tissues and able to explore their intimate relationships with the cellular replication machinery. The technology is being increasingly used to investigate how the plant RNA silencing mechanism attacks viral genomes and, recently, how viruses perturb the antiviral silencing machinery and induce symptoms expression. On the applied side, deep sequencing allowed to investigate diseases of unknown etiology, leading to the identification of new viruses, and to have an overview of the viral and viroids contents of a cultivated parcel (i.e the "virome" of a vineyard). Supported by dedicated bioinformatics tools it is now possible to assemble a complete viral genome thus envisaging the adoption of this unbiased approach for a diagnostic use. We have experienced the Illumina/Solexa system for the analysis of small RNAs populations, in healthy and virus-diseased grapevine plants. The techniques proved efficient for identifying a new virus in a widely diffused grapevine variety, whose detection would otherwise be difficult and time consuming.