title: Deep sequencing for discovery and evolutionary analysis of plant viruses.
abstract: The advent of next generation sequencing (NGS), or deep sequencing, has allowed great advances to be made in discovery, diagnostics, and evolutionary studies in plant viruses. Various methods have been used for enrichment for virus-specific nucleic acids, each of which have some drawbacks. Many novel viruses have been discovered in plants by NGS technologies, and there is a good deal of promise for more comprehensive studies in virus evolution. However, each aspect of using NGS has its caveats that need to be considered, and there is still a need for better tools of analysis, as well as method for validation of sequence variation.
authors.affiliation: Center for Infectious Disease Dynamics, Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, United States. Electronic address: mjr25@psu.edu.
authors.forename: Marilyn J
authors.initials: MJ
authors.lastname: Roossinck
mesh_terms: D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D025202:Molecular Diagnostic Techniques; D058889:Molecular Typing; D010935:Plant Diseases / Q000821:virology; D010942:Plant Viruses / Q000145:classification / Q000235:genetics*
keywords: Bioinformatics; Double-stranded RNA; Metagenomics; siRNA; virus-like particles