title: Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology.
abstract: A novel, unbiased approach to plant viral disease diagnosis has been developed which requires no a priori knowledge of the host or pathogen. Next-generation sequencing coupled with metagenomic analysis was used to produce large quantities of cDNA sequence in a model system of tomato infected with Pepino mosaic virus. The method was then applied to a sample of Gomphrena globosa infected with an unknown pathogen originally isolated from the flowering plant Liatris spicata. This plant was found to contain a new cucumovirus, for which we suggest the name 'Gayfeather mild mottle virus'. In both cases, the full viral genome was sequenced. This method expedites the entire process of novel virus discovery, identification, viral genome sequencing and, subsequently, the development of more routine assays for new viral pathogens.
authors.affiliation: Central Science Laboratory, Sand Hutton, York, UK. i.adams@csl.gov.uk
authors.forename: Ian P
authors.initials: IP
authors.lastname: Adams
authors.forename: Rachel H
authors.initials: RH
authors.lastname: Glover
authors.forename: Wendy A
authors.initials: WA
authors.lastname: Monger
authors.forename: Rick
authors.initials: R
authors.lastname: Mumford
authors.forename: Elena
authors.initials: E
authors.lastname: Jackeviciene
authors.forename: Meletele
authors.initials: M
authors.lastname: Navalinskiene
authors.forename: Marija
authors.initials: M
authors.lastname: Samuitiene
authors.forename: Neil
authors.initials: N
authors.lastname: Boonham
mesh_terms: D001483:Base Sequence; D023061:Gene Order; D016679:Genome, Viral / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D010942:Plant Viruses / Q000235:genetics* / Q000302:isolation & purification*; D010944:Plants / Q000821:virology*; D017422:Sequence Analysis, DNA / Q000379:methods*