Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests
Massart, Sebastien | Adams, Ian | Rwahnih, Al | Baeyen, Steve | Bilodeau, Guillaume, J | Blouin, Arnaud, G | Boonham, Neil | Candresse, Thierry | Chandellier, Anne | de Jonghe, Kris | Fox, Adrian | Gaafar, Yahya, Z A | Gentit, Pascal | Haegeman, Annelies | Ho, Wellcome | Hurtado-Gonzales, Oscar | Jonkers, Wilfried | Kreuze, Jan | Kutjnak, Denis | Landa, Blanca, B | Liu, Mingxin | Maclot, François | Malapi-Wight, Marta | Maree, Hans, J | Martoni, Francesco | Mehle, Natasa | Minafra, Angelantonio | Mollov, Dimitre | Moreira, Adriana, G | Nakhla, Mark | Petter, Françoise | Piper, Alexander, M | Ponchart, Julien, P | Rae, Robbie | Remenant, Benoit | Rivera, Yazmin | Rodoni, Brendan | Botermans, Marleen | Roenhorst, J.W. | Rollin, Johan | Saldarelli, Pasquale | Santala, Johanna | Souza-Richards, Rose | Spadaro, Davide | Studholme, David, J | Sultmanis, Stefanie | van der Vlugt, René | Tamisier, Lucie | Trontin, Charlotte | Vazquez-Iglesias, Ines | Vicente, Claudia, S L | van de Vossenberg, Bart, T L H | Westenberg, Marcel | Wetzel, Thierry | Ziebell, Heiko | Lebas, Benedicte, S M | Department Terra & AgroBioChem, Gembloux Agro‐Bio Tech ; Université de Liège = University of Liège = Universiteit van Luik = Universität Lüttich (ULiège) | Fera Science Ltd | University of California [Davis] (UC Davis) ; University of California (UC) | Research Institute for Agricultural, Fisheries and Food (ILVO) | Canadian Food Inspection Agency (CFIA) | Newcastle University [Newcastle] | Biologie du fruit et pathologie (BFP) ; Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Walloon Agricultural Research Centre | Julius Kühn-Institut (JKI) | Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES) | Ministry for Primary Industries | USDA-APHIS PPQ | Bejo Production | Consultative Group on International Agricultural Research [CGIAR] (CGIAR) | National Institute of Biology [Ljubljana] (NIB) | Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC) ; Consejo Superior de Investigaciones Cientificas [España] = Spanish National Research Council [Spain] (CSIC) | University of Tasmania [Hobart] (UTAS) | TERRA, Gembloux Agro-Bio Tech ; Gembloux Agro-Bio Tech [Faculté universitaire des sciences agronomiques de Gembloux] ([FUSAGx]) ; Université de Liège = University of Liège = Universiteit van Luik = Universität Lüttich (ULiège)-Université de Liège = University of Liège = Universiteit van Luik = Universität Lüttich (ULiège) | USDA Animal and Plant Health Inspection Service (USDA-APHIS) ; United States Department of Agriculture (USDA) | Stellenbosch University | Citrus Research International ; Partenaires INRAE | Agriculture Victoria (AgriBio) | CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP) ; National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR) | USDA-ARS : Agricultural Research Service | Food and Agriculture Organization of the United Nations [France] (FAO) ; Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO) | European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes (EPPO) | Liverpool John Moores University (LJMU) | Netherlands Food and Consumer Product Safety Authority (NVWA) | Finnish Food Authority ; Partenaires INRAE | International Seed Federation (ISF) | Università degli studi di Torino = University of Turin (UNITO) | University of Exeter | INIAV IP ; Partenaires INRAE | Dienstleistungszentrum Ländlicher Raum DLR Rheinpfalz (DLR Rheinpfalz)
International audience
Показать больше [+] Меньше [-]Английский. High-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.
Показать больше [+] Меньше [-]Библиографическая информация
Эту запись предоставил Institut national de la recherche agronomique