title: Plant Virus Metagenomics: Advances in Virus Discovery.
abstract: In recent years plant viruses have been detected from many environments, including domestic and wild plants and interfaces between these systems-aquatic sources, feces of various animals, and insects. A variety of methods have been employed to study plant virus biodiversity, including enrichment for virus-like particles or virus-specific RNA or DNA, or the extraction of total nucleic acids, followed by next-generation deep sequencing and bioinformatic analyses. All of the methods have some shortcomings, but taken together these studies reveal our surprising lack of knowledge about plant viruses and point to the need for more comprehensive studies. In addition, many new viruses have been discovered, with most virus infections in wild plants appearing asymptomatic, suggesting that virus disease may be a byproduct of domestication. For plant pathologists these studies are providing useful tools to detect viruses, and perhaps to predict future problems that could threaten cultivated plants.
authors.affiliation: First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors.forename: Marilyn J
authors.initials: MJ
authors.lastname: Roossinck
authors.affiliation: First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.affiliation: First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Roumagnac
mesh_terms: D000818:Animals; D044822:Biodiversity; D019295:Computational Biology; D004279:DNA, Viral / Q000235:genetics; D005243:Feces / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing; D007313:Insecta / Q000821:virology; D056186:Metagenomics; D010935:Plant Diseases / Q000821:virology*; D010942:Plant Viruses / Q000235:genetics*; D010944:Plants / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral