Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology.
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.
Adams
Ian P
IP
Central Science Laboratory, Sand Hutton, York, UK. i.adams@csl.gov.uk
Glover
Rachel H
RH
Monger
Wendy A
WA
Mumford
Rick
R
Jackeviciene
Elena
E
Navalinskiene
Meletele
M
Samuitiene
Marija
M
Boonham
Neil
N
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*