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Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

hal.structure.identifierUniversité de Liège - Gembloux
dc.contributor.authorMACLOT, François
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorFILLOUX, Denis
hal.structure.identifierMichigan State University [East Lansing]
dc.contributor.authorMALMSTROM, Carolyn
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorROUMAGNAC, Philippe
hal.structure.identifierWageningen University and Research [Wageningen] [WUR]
dc.contributor.authorVAN DER VLUGT, René
hal.structure.identifierUniversité de Liège - Gembloux
dc.contributor.authorMASSART, Sébastien
dc.date.issued2020
dc.identifier.issn1664-302X
dc.description.abstractEnThe ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.
dc.language.isoen
dc.publisherFrontiers Media
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectpathologie végétale
dc.subjectsanté des plantes
dc.subjectVirologie végétale
dc.subjectVirus phytopathogène
dc.subject.envirus ecology and evolution
dc.subject.enplant virome
dc.subject.enhigh throughput sequencing
dc.subject.enhistorical advances
dc.subject.enopportunities and challenges
dc.title.enIlluminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales
dc.typeArticle de revue
dc.typeArticle de synthèse
dc.identifier.doi10.3389/fmicb.2020.578064
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalFrontiers in Microbiology
bordeaux.page578064
bordeaux.volume11
bordeaux.peerReviewedoui
hal.identifierhal-02983693
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02983693v1
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