title: Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus.
abstract: The genetic diversity present in populations of RNA viruses is likely to be strongly modulated by aspects of their life history, including mode of transmission. However, how transmission mode shapes patterns of intra- and inter-host genetic diversity, particularly when acting in combination with de novo mutation, population bottlenecks and the selection of advantageous mutations, is poorly understood. To address these issues, this study performed ultradeep sequencing of zucchini yellow mosaic virus in a wild gourd, Cucurbita pepo ssp. texana, under two infection conditions: aphid vectored and mechanically inoculated, achieving a mean coverage of approximately 10 ,000×. It was shown that mutations persisted during inter-host transmission events in both the aphid vectored and mechanically inoculated populations, suggesting that the vector-imposed transmission bottleneck is not as extreme as previously supposed. Similarly, mutations were found to persist within individual hosts, arguing against strong systemic bottlenecks. Strikingly, mutations were seen to go to fixation in the aphid-vectored plants, suggestive of a major fitness advantage, but remained at low frequency in the mechanically inoculated plants. Overall, this study highlights the utility of ultradeep sequencing in providing high-resolution data capable of revealing the nature of virus evolution, particularly as the full spectrum of genetic diversity within a population may not be uncovered without sequence coverage of at least 2500-fold.
authors.affiliation: Seed Science Center, Iowa State University, Ames, IA 50011, USA.|Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: H E
authors.initials: HE
authors.lastname: Simmons
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: J P
authors.initials: JP
authors.lastname: Dunham
authors.affiliation: Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: J C
authors.initials: JC
authors.lastname: Stack
authors.affiliation: The Huck Institutes for the Life Sciences and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: B J A
authors.initials: BJA
authors.lastname: Dickins
authors.affiliation: Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, 28223, Pozuelo de Alarcón (Madrid), Spain.|Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: I
authors.initials: I
authors.lastname: Pagán
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.|Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: E C
authors.initials: EC
authors.lastname: Holmes
authors.affiliation: Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: A G
authors.initials: AG
authors.lastname: Stephenson
mesh_terms: D000818:Animals; D001042:Aphids / Q000821:virology; D001483:Base Sequence; D016384:Consensus Sequence; D028464:Cucurbita / Q000821:virology*; D014644:Genetic Variation; D016679:Genome, Viral; D007303:Insect Vectors; D008969:Molecular Sequence Data; D009029:Mosaic Viruses / Q000235:genetics*; D009154:Mutation; D010935:Plant Diseases / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D012367:RNA, Viral