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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
Author(s) -
Lebas Benedicte,
Adams Ian,
Al Rwahnih Maher,
Baeyen Steve,
Bilodeau Guillaume J.,
Blouin Arnaud G.,
Boonham Neil,
Candresse Thierry,
Chandelier Anne,
De Jonghe Kris,
Fox Adrian,
Gaafar Yahya Z. A.,
Gentit Pascal,
Haegeman Annelies,
Ho Wellcome,
HurtadoGonzales Oscar,
Jonkers Wilfried,
Kreuze Jan,
Kutjnak Denis,
Landa Blanca,
Liu Mingxin,
Maclot François,
MalapiWight Martha,
Maree Hano J.,
Martoni Francesco,
Mehle Natasha,
Minafra Angelantonio,
Mollov Dimitre,
Moreira Adriana,
Nakhla Mark,
Petter Françoise,
Piper Alexander M.,
Ponchart Julien,
Rae Robbie,
Remenant Benoit,
Rivera Yazmin,
Rodoni Brendan,
Roenhorst Johanna W.,
Rollin Johan,
Saldarelli Pasquale,
Santala Johanna,
SouzaRichards Rose,
Spadaro Davide,
Studholme David J.,
Sultmanis Stefanie,
Vlugt René,
Tamisier Lucie,
Trontin Charlotte,
VazquezIglesias Ines,
Vicente Claudia S. L.,
Vossenberg Bart T. L. H.,
Wetzel Thierry,
Ziebell Heiko,
Massart Sebastien
Publication year - 2022
Publication title -
eppo bulletin
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.327
H-Index - 36
eISSN - 1365-2338
pISSN - 0250-8052
DOI - 10.1111/epp.12863
Subject(s) - glossary , identification (biology) , plant quarantine , standardization , microbiology and biotechnology , amplicon sequencing , phytosanitary certification , computer science , biology , quarantine , ecology , philosophy , linguistics , genetics , 16s ribosomal rna , bacteria , horticulture , operating system
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.