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

Author

Sebastien Massart, Ian Adams, Maher Al Rwahnih, Steve Baeyen, Guillaume J. Bilodeau, Arnaud G. Blouin, Neil Boonham, Thierry Candresse, Anne Chandellier, Kris De Jonghe, Adrian Fox, Yahya Z.A. Gaafar, Pascal Gentit, Annelies Haegeman, Wellcome Ho, Oscar Hurtado-Gonzales, Wilfried Jonkers, Jan Kreuze, Denis Kutjnak, Blanca B. Landa, Mingxin Liu, François Maclot, Marta Malapi-Wight, Hans J. Maree, Francesco Martoni, Natasa Mehle, Angelantonio Minafra, Dimitre Mollov, Adriana G. Moreira, Mark Nakhla, Françoise Petter, Alexander M. Piper, Julien P. Ponchart, Robbie Rae, Benoit Remenant, Yazmin Rivera, Brendan Rodoni, Marleen Botermans, J.W. Roenhorst, Johan Rollin, Pasquale Saldarelli, Johanna Santala, Rose Souza-Richards, Davide Spadaro, David J. Studholme, Stefanie Sultmanis, René van der Vlugt, Lucie Tamisier, Charlotte Trontin, Ines Vazquez-Iglesias, Claudia S.L. Vicente, Bart T.L.H. van de Vossenberg, Marcel Westenberg, Thierry Wetzel, Heiko Ziebell, and Benedicte S. M. Lebas

Subjects
Biointeractions and Plant Health, fungi, food and beverages, Life Science, PE&RC
Abstract

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, mycetes, 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., Scientific publication adapted from the deliverable 2.2 of the Valitest project - www.valitest.eu

Published
2022
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2. Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories : A step-by-step description

Author

Benedicte Lebas, Ian Adams, Maher Al Rwahnih, Steve Baeyen, Guillaume J. Bilodeau, Arnaud G. Blouin, Neil Boonham, Thierry Candresse, Anne Chandelier, Kris De Jonghe, Adrian Fox, Yahya Z. A. Gaafar, Pascal Gentit, Annelies Haegeman, Wellcome Ho, Oscar Hurtado‐Gonzales, Wilfried Jonkers, Jan Kreuze, Denis Kutjnak, Blanca Landa, Mingxin Liu, François Maclot, Martha Malapi‐Wight, Hano J. Maree, Francesco Martoni, Natasha Mehle, Angelantonio Minafra, Dimitre Mollov, Adriana Moreira, Mark Nakhla, Françoise Petter, Alexander M. Piper, Julien Ponchart, Robbie Rae, Benoit Remenant, Yazmin Rivera, Brendan Rodoni, Johanna W. Roenhorst, Johan Rollin, Pasquale Saldarelli, Johanna Santala, Rose Souza‐Richards, Davide Spadaro, David J. Studholme, Stefanie Sultmanis, René van der Vlugt, Lucie Tamisier, Charlotte Trontin, Ines Vazquez‐Iglesias, Claudia S. L. Vicente, Bart T. L. H. Vossenberg, Thierry Wetzel, Heiko Ziebell, Sebastien Massart, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, 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), 1Walloon Agricultural Research Centre, Gembloux, Belgium 2The Research Institute of Organic Agriculture (FIBL), Frick, Switzerland, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants, 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), Ministry for Primary Industries, Animal Plant Health Inspection Service, APHIS-USDA, Humble, Texas, 77338, USA., World Agroforestry Center [CGIAR, Pérou] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), National Institute of Biology [Ljubljana] (NIB), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Tasmania [Hobart, Australia] (UTAS), 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), Horticultural Crops Research Unit, USDA-ARS : Agricultural Research Service, International Plant Protection Convention, 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, International Seed Federation (ISF), Università degli studi di Torino = University of Turin (UNITO), University of Exeter, Wageningen University and Research [Wageningen] (WUR), Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal] (INIAV), Dienstleistungszentrum Ländlicher Raum DLR Rheinpfalz (DLR Rheinpfalz), Julius Kühn-Institute, Federal Research Centre for Cultivated Plants-Institute for Biological Control, European Project: 773139,VALITEST, and European Commission

Subjects
plant pest diagnostic test, Biointeractions and Plant Health, [SDV]Life Sciences [q-bio], Life Science, high-throughput sequencing, Plant Science, Horticulture, PE&RC, Agronomy and Crop Science, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

High-throughput sequencing (HTS) is a powerful tool that enables the simultaneous detection and potential identification of any organisms present in a sample. The growing interest in the application of HTS technologies for routine diagnostics in plant health laboratories is triggering the development of guidelines on how to prepare laboratories for performing HTS testing. This paper describes general and technical recommendations to guide laboratories through the complex process of preparing a laboratory for HTS tests within existing quality assurance systems. From nucleic acid extractions to data analysis and interpretation, all of the steps are covered to ensure reliable and reproducible results. These guidelines are relevant for the detection and identification of any plant pest (e.g. arthropods, bacteria, fungi, nematodes, invasive plants or weeds, protozoa, viroids, viruses), and from any type of matrix (e.g. pure microbial culture, plant tissue, soil, water), regardless of the HTS technology (e.g. amplicon sequencing, shotgun sequencing) and of the application (e.g. surveillance programme, phytosanitary certification, quarantine, import control). These guidelines are written in general terms to facilitate the adoption of HTS technologies in plant pest routine diagnostics and enable broader application in all plant health fields, including research. A glossary of relevant terms is provided among the Supplementary Material., This article is based upon work from the work package 2 of the project VALITEST (https://www.valitest.eu/), supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 773139.

Published
2022
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