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

Benedicte S.M. 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 Gaafar, Pascal Gentit, Annelies Haegeman, W Ho, Oscar Hurtado-Gonzales, W Jonkers, Jan Kreuze, Denis Kutnjak, Blanca B. LandaM Liu, François Maclot, Martha Malapi-Wight, Hano Maree, F MArtoni, Natasa Mehle, Angelantonio Minafra, D Mollov, AG Moreira, M Nakhla, Françoise Petter, A.M. Piper, J.P. Ponchart, R. Rae, Benoit Remenant, Y. Rivera, B. Rodoni, Johanna W Roenhorst, Johan Rollin, P Saldarelli, Johanna Santala, Rose Souza-Richards, D Spadaro, D.J. Studholme, S. Sultmanis, René van der Vlugt, Lucie Tamisier, Charlotte Trontin, Ines Vazquez-Iglesias, C.S.L. Vicente, Bart T.L.H. van de Vossenberg, Thierry Wetzel, Heiko Ziebell, Sebastien Massart

Onderzoeksoutput: Bijdrage aan tijdschriftA2: Artikel in een internationaal wetenschappelijk tijdschrift met peer review, dat niet inbegrepen is in A1peer review


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.
Oorspronkelijke taalEngels
TijdschriftEPPO Bulletin
Pagina's (van-tot)394-418
Aantal pagina’s25
PublicatiestatusGepubliceerd - 1-aug.-2022


  • B390-fytopathologie


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