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Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests

hal.structure.identifierDepartment Terra & AgroBioChem, Gembloux Agro‐Bio Tech
dc.contributor.authorMASSART, Sebastien
hal.structure.identifierFera Science Ltd
dc.contributor.authorADAMS, Ian
hal.structure.identifierUniversity of California [Davis] [UC Davis]
dc.contributor.authorRWAHNIH, Al
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorBAEYEN, Steve
hal.structure.identifierCanadian Food Inspection Agency [CFIA]
dc.contributor.authorBILODEAU, Guillaume
hal.structure.identifierDepartment Terra & AgroBioChem, Gembloux Agro‐Bio Tech
dc.contributor.authorBLOUIN, Arnaud
hal.structure.identifierNewcastle University [Newcastle]
dc.contributor.authorBOONHAM, Neil
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
hal.structure.identifierWalloon Agricultural Research Centre
dc.contributor.authorCHANDELLIER, Anne
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorDE JONGHE, Kris
hal.structure.identifierFera Science Ltd
dc.contributor.authorFOX, Adrian
hal.structure.identifierJulius Kühn-Institut [JKI]
dc.contributor.authorGAAFAR, Yahya
hal.structure.identifierAgence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail [ANSES]
dc.contributor.authorGENTIT, Pascal
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorHAEGEMAN, Annelies
hal.structure.identifierMinistry for Primary Industries
dc.contributor.authorHO, Wellcome
hal.structure.identifierUSDA-APHIS PPQ
dc.contributor.authorHURTADO-GONZALES, Oscar
hal.structure.identifierBejo Production
dc.contributor.authorJONKERS, Wilfried
hal.structure.identifierConsultative Group on International Agricultural Research [CGIAR] [CGIAR]
dc.contributor.authorKREUZE, Jan
hal.structure.identifierNational Institute of Biology [Ljubljana] [NIB]
dc.contributor.authorKUTJNAK, Denis
hal.structure.identifierInstituto de Agricultura Sostenible - Institute for Sustainable Agriculture [IAS CSIC]
dc.contributor.authorLANDA, Blanca
hal.structure.identifierUniversity of Tasmania [Hobart, Australia] [UTAS]
dc.contributor.authorLIU, Mingxin
hal.structure.identifierTERRA, Gembloux Agro-Bio Tech
dc.contributor.authorMACLOT, François
hal.structure.identifierUSDA Animal and Plant Health Inspection Service [USDA-APHIS]
dc.contributor.authorMALAPI-WIGHT, Marta
hal.structure.identifierStellenbosch University
hal.structure.identifierCitrus Research International
dc.contributor.authorMAREE, Hans
hal.structure.identifierAgriculture Victoria [AgriBio]
dc.contributor.authorMARTONI, Francesco
hal.structure.identifierNational Institute of Biology [Ljubljana] [NIB]
dc.contributor.authorMEHLE, Natasa
hal.structure.identifierCNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP]
dc.contributor.authorMINAFRA, Angelantonio
hal.structure.identifierUSDA-ARS : Agricultural Research Service
dc.contributor.authorMOLLOV, Dimitre
hal.structure.identifierFood and Agriculture Organization of the United Nations [FAO]
dc.contributor.authorMOREIRA, Adriana
hal.structure.identifierUSDA-APHIS PPQ
dc.contributor.authorNAKHLA, Mark
hal.structure.identifierEuropean and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes [EPPO]
dc.contributor.authorPETTER, Françoise
hal.structure.identifierAgriculture Victoria [AgriBio]
dc.contributor.authorPIPER, Alexander
hal.structure.identifierTERRA, Gembloux Agro-Bio Tech
dc.contributor.authorPONCHART, Julien
hal.structure.identifierLiverpool John Moores University [LJMU]
dc.contributor.authorRAE, Robbie
hal.structure.identifierAgence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail [ANSES]
dc.contributor.authorREMENANT, Benoit
hal.structure.identifierUSDA-APHIS PPQ
dc.contributor.authorRIVERA, Yazmin
hal.structure.identifierAgriculture Victoria [AgriBio]
dc.contributor.authorRODONI, Brendan
hal.structure.identifierNetherlands Food and Consumer Product Safety Authority [NVWA]
dc.contributor.authorBOTERMANS, Marleen
hal.structure.identifierNetherlands Food and Consumer Product Safety Authority [NVWA]
dc.contributor.authorROENHORST, J.W.
hal.structure.identifierTERRA, Gembloux Agro-Bio Tech
dc.contributor.authorROLLIN, Johan
hal.structure.identifierCNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP]
dc.contributor.authorSALDARELLI, Pasquale
hal.structure.identifierFinnish Food Authority
dc.contributor.authorSANTALA, Johanna
hal.structure.identifierInternational Seed Federation [ISF]
dc.contributor.authorSOUZA-RICHARDS, Rose
hal.structure.identifierUniversità degli studi di Torino = University of Turin [UNITO]
dc.contributor.authorSPADARO, Davide
hal.structure.identifierUniversity of Exeter
dc.contributor.authorSTUDHOLME, David
hal.structure.identifierCanadian Food Inspection Agency [CFIA]
dc.contributor.authorSULTMANIS, Stefanie
hal.structure.identifierINIAV IP
dc.contributor.authorVAN DER VLUGT, René
hal.structure.identifierTERRA, Gembloux Agro-Bio Tech
dc.contributor.authorTAMISIER, Lucie
hal.structure.identifierEuropean and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes [EPPO]
dc.contributor.authorTRONTIN, Charlotte
hal.structure.identifierFera Science Ltd
dc.contributor.authorVAZQUEZ-IGLESIAS, Ines
hal.structure.identifierINIAV IP
dc.contributor.authorVICENTE, Claudia
hal.structure.identifierNetherlands Food and Consumer Product Safety Authority [NVWA]
dc.contributor.authorVAN DE VOSSENBERG, Bart
hal.structure.identifierNetherlands Food and Consumer Product Safety Authority [NVWA]
dc.contributor.authorWESTENBERG, Marcel
hal.structure.identifierDienstleistungszentrum Ländlicher Raum DLR Rheinpfalz [DLR Rheinpfalz]
dc.contributor.authorWETZEL, Thierry
hal.structure.identifierJulius Kühn-Institut [JKI]
dc.contributor.authorZIEBELL, Heiko
hal.structure.identifierTERRA, Gembloux Agro-Bio Tech
dc.contributor.authorLEBAS, Benedicte
dc.date.issued2022-10-25
dc.identifier.issn2804-3871
dc.description.abstractEnHigh-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, confirming and interpreting results. These guidelines cover any HTS test used for the detection and identification of any plant pest (viroid, virus, bacteria, phytoplasma, fungi and fungus-like protists, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health.
dc.language.isoen
dc.publisherPeer Community In
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enHigh-throughput sequencing HTS
dc.title.enGuidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests
dc.typeArticle de revue
dc.identifier.doi10.24072/pci.infections.100002
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalPeer Community Journal
bordeaux.pagee62
bordeaux.volume2
bordeaux.peerReviewedoui
hal.identifierhal-03915292
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03915292v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Peer%20Community%20Journal&rft.date=2022-10-25&rft.volume=2&rft.spage=e62&rft.epage=e62&rft.eissn=2804-3871&rft.issn=2804-3871&rft.au=MASSART,%20Sebastien&ADAMS,%20Ian&RWAHNIH,%20Al&BAEYEN,%20Steve&BILODEAU,%20Guillaume&rft.genre=article


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