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A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses

hal.structure.identifierNational Institute of Biology [Ljubljana] [NIB]
dc.contributor.authorKUTNJAK, Denis
hal.structure.identifierGembloux Agro-Bio Tech [Faculté universitaire des sciences agronomiques de Gembloux] [[FUSAGx]]
dc.contributor.authorTAMISIER, Lucie
hal.structure.identifierFera Science Limited
dc.contributor.authorADAMS, Ian
hal.structure.identifierNewcastle University [Newcastle]
dc.contributor.authorBOONHAM, Neil
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
hal.structure.identifierCNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP]
dc.contributor.authorCHIUMENTI, Michela
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorDE JONGHE, Kris
hal.structure.identifierInternational Potato Center [Lima] [CIP]
dc.contributor.authorKREUZE, Jan F.
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorLEFEBVRE, Marie
hal.structure.identifierNatural Resources Institute (NRI), University of Greenwich, UK
dc.contributor.authorSILVA, Goncalo
hal.structure.identifierUnited States Department of Agriculture - Animal and Plant Health Inspection Service
dc.contributor.authorMALAPI-WIGHT, Martha
hal.structure.identifierLeibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures [DSMZ]
dc.contributor.authorMARGARIA, Paolo
hal.structure.identifierUniversity of Maribor
dc.contributor.authorMAVRIC PLESCO, Irena
hal.structure.identifierFera Science Limited
dc.contributor.authorMCGREIG, Sam
hal.structure.identifierCNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP]
dc.contributor.authorMIOZZI, Laura
hal.structure.identifierLaboratoire de santé des végétaux [LSV Angers]
dc.contributor.authorREMENANT, Benoit
hal.structure.identifierAgroscope
dc.contributor.authorREYNARD, Jean Sebastien
hal.structure.identifierGembloux Agro-Bio Tech [Faculté universitaire des sciences agronomiques de Gembloux] [[FUSAGx]]
hal.structure.identifierDNA Vision SA
dc.contributor.authorROLLIN, Johan
hal.structure.identifierCanadian Food Inspection Agency [CFIA]
dc.contributor.authorROTT, Mike
hal.structure.identifierAgroscope
dc.contributor.authorSCHUMPP, Olivier
hal.structure.identifierGembloux Agro-Bio Tech [Faculté universitaire des sciences agronomiques de Gembloux] [[FUSAGx]]
dc.contributor.authorMASSART, Sébastien
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorHAEGEMAN, Annelies
dc.date.issued2021-04-14
dc.identifier.issn2076-2607
dc.description.abstractEnHigh-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects
dc.language.isoen
dc.publisherMDPI
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectPathologie Végétale
dc.subjectVirologie végétale
dc.subjectSanté des plantes
dc.subject.enplant virus
dc.subject.enhigh-throughput sequencing
dc.subject.enbioinformatics
dc.subject.endetection
dc.subject.endiscovery
dc.title.enA Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
dc.typeArticle de revue
dc.typeArticle de synthèse
dc.identifier.doi10.3390/microorganisms9040841
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalMicroorganisms
bordeaux.page841
bordeaux.volume9
bordeaux.issue4
bordeaux.peerReviewedoui
hal.identifierhal-03200602
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03200602v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Microorganisms&rft.date=2021-04-14&rft.volume=9&rft.issue=4&rft.spage=841&rft.epage=841&rft.eissn=2076-2607&rft.issn=2076-2607&rft.au=KUTNJAK,%20Denis&TAMISIER,%20Lucie&ADAMS,%20Ian&BOONHAM,%20Neil&CANDRESSE,%20Thierry&rft.genre=article&unknown


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