Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard

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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. © 2010 Elsevier Inc.

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Coetzee, B., Freeborough, M. J., Maree, H. J., Celton, J. M., Rees, D. J. G., & Burger, J. T. (2010). Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard. Virology, 400(2), 157–163. https://doi.org/10.1016/j.virol.2010.01.023

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