Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests
Sebastien Massart
(1)
,
Ian Adams
(2)
,
Al Rwahnih
(3)
,
Steve Baeyen
(4)
,
Guillaume J Bilodeau
(5)
,
Arnaud G Blouin
(1)
,
Neil Boonham
(6)
,
Thierry Candresse
(7)
,
Anne Chandellier
(8)
,
Kris de Jonghe
(4)
,
Adrian Fox
(2)
,
Yahya Z A Gaafar
(9)
,
Pascal Gentit
(10)
,
Annelies Haegeman
(4)
,
Wellcome Ho
(11)
,
Oscar Hurtado-Gonzales
(12)
,
Wilfried Jonkers
(13)
,
Jan Kreuze
(14)
,
Denis Kutjnak
(15)
,
Blanca B Landa
(16)
,
Mingxin Liu
(17)
,
François Maclot
(18)
,
Marta Malapi-Wight
(19)
,
Hans J Maree
(20, 21)
,
Francesco Martoni
(22)
,
Natasa Mehle
(15)
,
Angelantonio Minafra
(23)
,
Dimitre Mollov
(24)
,
Adriana G Moreira
(25)
,
Mark Nakhla
(12)
,
Françoise Petter
(26)
,
Alexander M Piper
(22)
,
Julien P Ponchart
(18)
,
Robbie Rae
(27)
,
Benoit Remenant
(10)
,
Yazmin Rivera
(12)
,
Brendan Rodoni
(22)
,
Marleen Botermans
(28)
,
J.W. Roenhorst
(28)
,
Johan Rollin
(18)
,
Pasquale Saldarelli
(23)
,
Johanna Santala
(29)
,
Rose Souza-Richards
(30)
,
Davide Spadaro
(31)
,
David J Studholme
(32)
,
Stefanie Sultmanis
(5)
,
René van der Vlugt
(33)
,
Lucie Tamisier
(18)
,
Charlotte Trontin
(26)
,
Ines Vazquez-Iglesias
(2)
,
Claudia S L Vicente
(33)
,
Bart T L H van de Vossenberg
(28)
,
Marcel Westenberg
(28)
,
Thierry Wetzel
(34)
,
Heiko Ziebell
(9)
,
Benedicte S M Lebas
(18)
1
Department Terra & AgroBioChem, Gembloux Agro‐Bio Tech
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 Walloon Agricultural Research Centre
9 JKI - Julius Kühn-Institut
10 ANSES - Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail
11 Ministry for Primary Industries
12 USDA-APHIS PPQ
13 Bejo Production
14 CGIAR - Consultative Group on International Agricultural Research [CGIAR]
15 NIB - National Institute of Biology [Ljubljana]
16 IAS CSIC - Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture
17 UTAS - University of Tasmania [Hobart, Australia]
18 TERRA, Gembloux Agro-Bio Tech
19 USDA-APHIS - USDA Animal and Plant Health Inspection Service
20 Stellenbosch University
21 Citrus Research International
22 AgriBio - Agriculture Victoria
23 IPSP - CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia]
24 USDA-ARS : Agricultural Research Service
25 FAO - Food and Agriculture Organization of the United Nations
26 EPPO - European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes
27 LJMU - Liverpool John Moores University
28 NVWA - Netherlands Food and Consumer Product Safety Authority
29 Finnish Food Authority
30 ISF - International Seed Federation
31 UNITO - Università degli studi di Torino = University of Turin
32 University of Exeter
33 INIAV IP
34 DLR Rheinpfalz - Dienstleistungszentrum Ländlicher Raum DLR Rheinpfalz
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 Walloon Agricultural Research Centre
9 JKI - Julius Kühn-Institut
10 ANSES - Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail
11 Ministry for Primary Industries
12 USDA-APHIS PPQ
13 Bejo Production
14 CGIAR - Consultative Group on International Agricultural Research [CGIAR]
15 NIB - National Institute of Biology [Ljubljana]
16 IAS CSIC - Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture
17 UTAS - University of Tasmania [Hobart, Australia]
18 TERRA, Gembloux Agro-Bio Tech
19 USDA-APHIS - USDA Animal and Plant Health Inspection Service
20 Stellenbosch University
21 Citrus Research International
22 AgriBio - Agriculture Victoria
23 IPSP - CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia]
24 USDA-ARS : Agricultural Research Service
25 FAO - Food and Agriculture Organization of the United Nations
26 EPPO - European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes
27 LJMU - Liverpool John Moores University
28 NVWA - Netherlands Food and Consumer Product Safety Authority
29 Finnish Food Authority
30 ISF - International Seed Federation
31 UNITO - Università degli studi di Torino = University of Turin
32 University of Exeter
33 INIAV IP
34 DLR Rheinpfalz - Dienstleistungszentrum Ländlicher Raum DLR Rheinpfalz
Thierry Candresse
- Fonction : Auteur
- PersonId : 741063
- IdHAL : thierry-candresse
- ORCID : 0000-0001-9757-1835
- IdRef : 058616438
Lucie Tamisier
- Fonction : Auteur
- PersonId : 743361
- IdHAL : lucie-tamisier
- ORCID : 0000-0002-9231-2997
- IdRef : 224559699
Résumé
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, fungi and fungus-like protists, 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.
Origine : Fichiers éditeurs autorisés sur une archive ouverte
