title: Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard.
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.
authors.affiliation: Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa.
authors.forename: Beatrix
authors.initials: B
authors.lastname: Coetzee
authors.forename: Michael-John
authors.initials: MJ
authors.lastname: Freeborough
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Maree
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Celton
authors.forename: D Jasper G
authors.initials: DJ
authors.lastname: Rees
authors.forename: Johan T
authors.initials: JT
authors.lastname: Burger
mesh_terms: D044822:Biodiversity; D054892:Metagenome; D010802:Phylogeny; D010942:Plant Viruses / Q000145:classification* / Q000235:genetics*; D012330:RNA, Double-Stranded / Q000235:genetics / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D013019:South Africa; D027843:Vitis / Q000821:virology*
chemical_list: D012330:RNA, Double-Stranded; D012367:RNA, Viral