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

Sébastien Massart*, Ian Adams, M. 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, D. Kutnjak, Blanca LandaM. Liu, François Maclot, Martha Malapi-Wight, Hano J. Maree, Francesco Martoni, Nataša Mehle, Angelantonio Minafra, Dimitre Mollov, Adriana Moreira, Mark Nakhla, F. Petter, Alexander M. Piper, Julien Ponchart, Robbie Rae, Benoit Remenant, Yazmin Rivera, Brendan Rodoni, M. Boterans, J.W. Roenhorst, Johan Rollin, Pasquale Saldarelli, Johanna Santala, Rose Souza-Richards, Davide Spadaro, David J. Studholme, Stefanie Sultmanis, R.A.A. van der Vlugt, Lucie Tamisier, C. Trontin, Ines Vazquez-Iglesias, Claudia S.L. Vicente, Bart T.L.H. Vossenberg, Marcel Westenberg, Thierry Wetzel, Heiko Ziebell, Benedicte Lebas

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


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.
Original languageEnglish
Article numbere62
JournalPeer Community Journal
Publication statusPublished - 30 Sept 2022


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