A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
2021
Kutnjak, Denis | Tamisier, Lucie | Adams, Ian | Boonham, Neil | Candresse, Thierry | Chiumenti, Michela | de Jonghe, Kris | Kreuze, Jan F. | Lefebvre, Marie | Silva, Goncalo | Malapi-Wight, Martha | Margaria, Paolo | Mavric Plesco, Irena | Mcgreig, Sam | Miozzi, Laura | Remenant, Benoit | Reynard, Jean Sebastien | Rollin, Johan | Rott, Mike | Schumpp, Olivier | Massart, Sébastien | Haegeman, Annelies | National Institute of Biology [Ljubljana] (NIB) | Gembloux Agro-Bio Tech [Faculté universitaire des sciences agronomiques de Gembloux] ([FUSAGx]) ; Université de Liège = University of Liège = Universiteit van Luik = Universität Lüttich (ULiège) | Fera Science Limited | 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) | CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP) ; National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR) | Research Institute for Agricultural, Fisheries and Food (ILVO) | International Potato Center [Lima] (CIP) ; International Potato Center = Centre International de la Pomme de terre (CIP) ; Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR) | Natural Resources Institute (NRI), University of Greenwich, UK | United States Department of Agriculture - Animal and Plant Health Inspection Service ; Partenaires INRAE | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ) | University of Maribor | Laboratoire de santé des végétaux (LSV Angers) ; Laboratoire de la santé des végétaux (LSV) ; Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES) | Agroscope | DNA Vision SA | Canadian Food Inspection Agency (CFIA) | This review was partially funded by the Belgian Federal Public Service of Health, Food Chain Safety and Environment (FPS Health) through the contract “RI 18_A-289”, Slovenian Research Agency (core funding P4-0407, P4-0072 and project L7-2632), by the Euphresco project “Plant Health Bioinformatics Network” (PHBN) (2018-A-289), the CGIAR research program on roots, tubers and bananas (http://www.cgiar.org/about-us/ourfunders/, accessed on 13 April 2021) and the Bill & Melinda Gates foundation (investment ID OPP1130216).
International audience
Show more [+] Less [-]English. High-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
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