Vineyardomics: SOS – Save our Shiraz!

Shiraz Grapevines are an important global crop which are widely planted throughout temperate regions. Viruses are a significant factor in reducing the quality and quantity of the yield and are known to reduce the productive life of vineyards. Grapevines are subject to infection by more than 60 different viruses, the most known for any crop plant. Most important grapevine virus diseases are caused by complexes of viruses, with up to nine different viruses having been identified in a single vine. In South Africa, as in most grape-growing regions of the world, grapevine leafroll is regarded to be the most significant virus disease affecting grapevine, with Shiraz disease and Shiraz decline becoming more prominent as emerging diseases in the industry.

Present disease diagnostics rely on ELISA or RT-PCR and target the viruses that have historically been associated with these diseases. While these tests are highly specific, they may not result in an accurate reflection of the etiological status of the tested plant, or of the particular disease, since none of the current diagnostic techniques address the potential contribution of other known or unknown viruses that may be involved in the etiology of a particular disease. Moreover, the error prone replication of RNA viruses leads to quasispecies, which can further complicate PCR-based detection assays as not all variants of the virus may be detected.

New and powerful technologies which are able to sequence viruses from environmental samples without the need for laborious and costly purification, cloning and screening techniques can result in the generation of sequence information for the complete virome in an unbiased fashion. This paper describes the use of sequencing-by-synthesis technology on the massively parallel Illumina Genome Analyzer II, to sequence an environmental sample composed of 44 randomly selected vines, to determine the virus profile of a severely diseased vineyard.

Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard. Virology. Feb 19 2010
Double stranded RNA, isolated from 44 pooled randomly selected vines from a diseased South African vineyard, has been used in a deep sequencing analysis to build a census of the viral population. The dsRNA was sequenced in an unbiased manner using the sequencing-by-synthesis technology offered by the Illumina Genome Analyzer II and yielded 837 megabases of metagenomic sequence data. Four known viral pathogens were identified. It was found that Grapevine leafroll-associated virus 3 (GLRaV-3) is the most prevalent species, constituting 59% of the total reads, followed by Grapevine rupestris stem pitting-associated virus and Grapevine virus A. Grapevine virus E, a virus not previously reported in South African vineyards, was identified in the census. Viruses not previously identified in grapevine were also detected. The second most prevalent virus detected was a member of the Chrysoviridae family similar to Penicillium chrysogenum virus. Sequences aligning to two other mycoviruses were also detected.

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