title: RNA-Seq reveals virus-virus and virus-plant interactions in nature.
abstract: As research on plant viruses has focused mainly on crop diseases, little is known about these viruses in natural environments. To understand the ecology of viruses in natural systems, comprehensive information on virus-virus and virus-host interactions is required. We applied RNA-Seq to plants from a natural population of Arabidopsis halleri subsp. gemmifera to simultaneously determine the presence/absence of all sequence-reported viruses, identify novel viruses and quantify the host transcriptome. By introducing the criteria of read number and genome coverage, we detected infections by Turnip mosaic virus (TuMV), Cucumber mosaic virus and Brassica yellows virus Active TuMV replication was observed by ultramicroscopy. De novo assembly further identified a novel partitivirus, Arabidopsis halleri partitivirus 1 Interestingly, virus reads reached a maximum level that was equivalent to that of the host's total mRNA, although asymptomatic infection was common. AhgAGO2, a key gene in host defence systems, was upregulated in TuMV-infected plants. Multiple infection was frequent in TuMV-infected leaves, suggesting that TuMV facilitates multiple infection, probably by suppressing host RNA silencing. Revealing hidden plant-virus interactions in nature can enhance our understanding of biological interactions and may have agricultural applications.
authors.affiliation: Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan kamitani@ecology.kyoto-u.ac.jp.
authors.forename: Mari
authors.initials: M
authors.lastname: Kamitani
authors.affiliation: Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2914, Japan JST PRESTO, Japan Science and Technology Agency, Honcho, Kawaguchi, Saitama 332-0012, Japan.
authors.forename: Atsushi J
authors.initials: AJ
authors.lastname: Nagano
authors.affiliation: Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan.
authors.forename: Mie N
authors.initials: MN
authors.lastname: Honjo
authors.affiliation: Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kudoh
mesh_terms: D017360:Arabidopsis / Q000821:virology*; D029681:Arabidopsis Proteins / Q000235:genetics*; D060565:Argonaute Proteins / Q000235:genetics*; D001483:Base Sequence; D001937:Brassica / Q000821:virology*; D016679:Genome, Viral / Q000235:genetics; D010935:Plant Diseases / Q000821:virology*; D018515:Plant Leaves / Q000821:virology; D017800:Potyvirus / Q000472:pathogenicity*; D012313:RNA; D012333:RNA, Messenger / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D012333:RNA, Messenger; D012367:RNA, Viral; C559855:argonaute 2 protein, Arabidopsis; D012313:RNA
keywords: Arabidopsis halleri; Arabidopsis halleri partitivirus 1; Argonaute2; RNA-Seq; Turnip mosaic virus; multiple infection