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Facilitating the adoption of high‐throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step‐by‐step description

2022; Wiley; Volume: 52; Issue: 2 Linguagem: Inglês

10.1111/epp.12863

1365-2338

B. S. M. Lebas, Ian P. 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 P. Hurtado‐Gonzales, Wilfried Jonkers, Jan Kreuze, Denis Kutjnak, Blanca B. Landa, Mingxin Liu, François Maclot, Martha Malapi‐Wight, Hans J. Maree, Francesco Martoni, Natasha Mehle, A. Minafra, Dimitre Mollov, Adriana Gonçalves Moreira, Mark K. Nakhla, Françoise Petter, Alexander M. Piper, Julien Ponchart, Robbie Rae, Benoît Remenant, Yazmín Rivera, Brendan Rodoni, J. W. Roenhorst, Johan Rollin, Pasquale Saldarelli, Johanna Santala, Rose Souza‐Richards, D. Spadaro, David J. Studholme, Stefanie Sultmanis, R.A.A. van der Vlugt, Lucie Tamisier, Charlotte Trontin, Ines Vazquez‐Iglesias, Cláudia S. L. Vicente, Bart van de Vossenberg, Thierry Wetzel, Heiko Ziebell, Sébastien Massart,

Plant Virus Research Studies

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.