Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard |
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Authors: | Beatrix Coetzee Hans J. Maree D. Jasper G. Rees |
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Affiliation: | a Department of Genetics, Stellenbosch University, Private Bag X1 Matieland, 7602, South Africa b Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa |
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Abstract: | 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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Keywords: | Metagenomic sequencing Deep sequencing analysis Grapevine viruses |
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