Facilitating the adoption of high‐throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step‐by‐step description
Benedicte Lebas
(1)
,
Ian Adams
(2)
,
Maher Al Rwahnih
(3)
,
Steve Baeyen
(4)
,
Guillaume J. Bilodeau
(5)
,
Arnaud Blouin
(1)
,
Neil Boonham
(6)
,
Thierry Candresse
(7)
,
Anne Chandelier
(8)
,
Kris de Jonghe
(4)
,
Adrian Fox
(2)
,
Yahya Gaafar
(9)
,
Pascal Gentit
(10)
,
Annelies Haegeman
(4)
,
Wellcome Ho
(11)
,
Oscar Hurtado-Gonzales
(12)
,
Wilfried Jonkers
,
Jan Kreuze
(13)
,
Denis Kutjnak
(14)
,
Blanca Landa
(15)
,
Mingxin Liu
(16)
,
François Maclot
(1)
,
Martha Malapi-Wight
(12)
,
Hano Maree
(17, 18)
,
Francesco Martoni
(19)
,
Natasha Mehle
(14)
,
Angelantonio Minafra
(20)
,
Dimitre Mollov
(21)
,
Adriana Moreira
(22)
,
Mark Nakhla
(12)
,
Françoise Petter
(23)
,
Alexander Piper
(19)
,
Julien Ponchart
(1)
,
Robbie Rae
(24)
,
Benoit Remenant
(10)
,
Yazmin Rivera
(12)
,
Brendan Rodoni
(19)
,
Johanna W. Roenhorst
(25)
,
Johan Rollin
(1)
,
Pasquale Saldarelli
(20)
,
Johanna Santala
(26)
,
Rose Souza-Richards
(27)
,
Davide Spadaro
(28)
,
David Studholme
(29)
,
Stefanie Sultmanis
(5)
,
René van der Vlugt
(30)
,
Lucie Tamisier
(1)
,
Charlotte Trontin
(23)
,
Ines Vazquez-Iglesias
(2)
,
Claudia Vicente
(31)
,
Bart Vossenberg
(25)
,
Thierry Wetzel
(32)
,
Heiko Ziebell
(33)
,
Sebastien Massart
(1)
1
Gembloux Agro-Bio Tech [Gembloux]
2 Fera Science Ltd
3 UC Davis - University of California [Davis]
4 ILVO - Research Institute for Agricultural, Fisheries and Food
5 CFIA - Canadian Food Inspection Agency
6 Newcastle University [Newcastle]
7 BFP - Biologie du fruit et pathologie
8 1Walloon Agricultural Research Centre, Gembloux, Belgium 2The Research Institute of Organic Agriculture (FIBL), Frick, Switzerland
9 Institute for Epidemiology and Pathogen Diagnostics
10 LSV Angers - Laboratoire de santé des végétaux
11 Ministry for Primary Industries
12 Animal Plant Health Inspection Service, APHIS-USDA, Humble, Texas, 77338, USA.
13 ICRAF - World Agroforestry Center [CGIAR, Pérou]
14 NIB - National Institute of Biology [Ljubljana]
15 CSIC - Centro de Investigaciones Biológicas
16 UTAS - University of Tasmania [Hobart, Australia]
17 Stellenbosch University
18 Citrus Research International
19 AgriBio - Agriculture Victoria
20 IPSP - CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia]
21 Horticultural Crops Research Unit
22 International Plant Protection Convention
23 EPPO - European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes
24 LJMU - Liverpool John Moores University
25 NVWA - Netherlands Food and Consumer Product Safety Authority
26 Finnish Food Authority
27 ISF - International Seed Federation
28 UNITO - Università degli studi di Torino = University of Turin
29 University of Exeter
30 WUR - Wageningen University and Research [Wageningen]
31 INIAV - Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal]
32 DLR Rheinpfalz - Dienstleistungszentrum Ländlicher Raum DLR Rheinpfalz
33 Julius Kühn-Institute
2 Fera Science Ltd
3 UC Davis - University of California [Davis]
4 ILVO - Research Institute for Agricultural, Fisheries and Food
5 CFIA - Canadian Food Inspection Agency
6 Newcastle University [Newcastle]
7 BFP - Biologie du fruit et pathologie
8 1Walloon Agricultural Research Centre, Gembloux, Belgium 2The Research Institute of Organic Agriculture (FIBL), Frick, Switzerland
9 Institute for Epidemiology and Pathogen Diagnostics
10 LSV Angers - Laboratoire de santé des végétaux
11 Ministry for Primary Industries
12 Animal Plant Health Inspection Service, APHIS-USDA, Humble, Texas, 77338, USA.
13 ICRAF - World Agroforestry Center [CGIAR, Pérou]
14 NIB - National Institute of Biology [Ljubljana]
15 CSIC - Centro de Investigaciones Biológicas
16 UTAS - University of Tasmania [Hobart, Australia]
17 Stellenbosch University
18 Citrus Research International
19 AgriBio - Agriculture Victoria
20 IPSP - CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia]
21 Horticultural Crops Research Unit
22 International Plant Protection Convention
23 EPPO - European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes
24 LJMU - Liverpool John Moores University
25 NVWA - Netherlands Food and Consumer Product Safety Authority
26 Finnish Food Authority
27 ISF - International Seed Federation
28 UNITO - Università degli studi di Torino = University of Turin
29 University of Exeter
30 WUR - Wageningen University and Research [Wageningen]
31 INIAV - Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal]
32 DLR Rheinpfalz - Dienstleistungszentrum Ländlicher Raum DLR Rheinpfalz
33 Julius Kühn-Institute
Thierry Candresse
- Fonction : Auteur
- PersonId : 741063
- IdHAL : thierry-candresse
- ORCID : 0000-0001-9757-1835
- IdRef : 058616438
Wilfried Jonkers
- Fonction : Auteur
Lucie Tamisier
- Fonction : Auteur
- PersonId : 743361
- IdHAL : lucie-tamisier
- ORCID : 0000-0002-9231-2997
- IdRef : 224559699
Claudia Vicente
- Fonction : Auteur
- PersonId : 183009
- IdHAL : vicente-claudia
- ORCID : 0000-0001-8205-6486
Résumé
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.