title: Metagenomic next-generation sequencing of viruses infecting grapevines.
abstract: Next-generation sequencing (NGS) technologies, for the first time, provide a truly "complete" representation of the viral (and other) pathogens present in a host organism. This is achieved in an unbiased way, and without any prior biological or molecular knowledge of these pathogen(s). During recent years a number of broad approaches, for most of the popular NGS platforms, have been developed. Here we describe such a protocol-one that accurately and reliably analyze viruses (and viroids) infecting grapevine. Our strategy relies on the synthesis of cDNA sequencing libraries from dsRNA, extracted from diseased grapevine tissues; the sequencing of these on an Illumina platform, and a streamlined bioinformatics pipeline to analyze the NGS data, yielding the virus composition (virome) of a specific grapevine tissue type, organ, entire plant, or even a vineyard.
authors.affiliation: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa, jtb@sun.ac.za.
authors.forename: Johan T
authors.initials: JT
authors.lastname: Burger
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Maree
mesh_terms: D019295:Computational Biology / Q000379:methods; D004279:DNA, Viral / Q000032:analysis* / Q000235:genetics; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D056186:Metagenomics; D010942:Plant Viruses / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA / Q000379:methods*; D027843:Vitis / Q000821:virology*
chemical_list: D004279:DNA, Viral