Section: Infections
Topic: Biology of interactions, Plant biology, Genetics/Genomics

Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests

10.24072/pcjournal.181 - Peer Community Journal, Volume 2 (2022), article no. e62.

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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.

Published online:
DOI: 10.24072/pcjournal.181
Type: Opinion, perspective
Massart, Sebastien 1; Adams, Ian 2; Al Rwahnih, Maher 3; Baeyen, Steve 4; Bilodeau, Guillaume J. 5; Blouin, Arnaud G. 1; Boonham, Neil 6; Candresse, Thierry 7; Chandellier, Anne 8; De Jonghe, Kris 4; Fox, Adrian 2; Gaafar, Yahya Z.A. 9; Gentit, Pascal 10; Haegeman, Annelies 4; Ho, Wellcome 11; Hurtado-Gonzales, Oscar 12; Jonkers, Wilfried 13; Kreuze, Jan 14; Kutjnak, Denis 15; Landa, Blanca B. 16; Liu, Mingxin 17; Maclot, François 1; Malapi-Wight, Marta 18; Maree, Hans J. 19, 20; Martoni, Francesco 21; Mehle, Natasa 15, 22; Minafra, Angelantonio 23; Mollov, Dimitre 24; Moreira, Adriana G. 25; Nakhla, Mark 26; Petter, Françoise 27; Piper, Alexander M. 21; Ponchart, Julien P. 1, 28; Rae, Robbie 29; Remenant, Benoit 10; Rivera, Yazmin 26; Rodoni, Brendan 21; Botermans, Marleen 30; Roenhorst, J.W. 30; Rollin, Johan 1; Saldarelli, Pasquale 23; Santala, Johanna 31; Souza-Richards, Rose 32; Spadaro, Davide 33; Studholme, David J. 34; Sultmanis, Stefanie 5; van der Vlugt, René 35; Tamisier, Lucie 1; Trontin, Charlotte 27; Vazquez-Iglesias, Ines 2; Vicente, Claudia S.L. 36; van de Vossenberg, Bart T.L.H. 30; Westenberg, Marcel 30; Wetzel, Thierry 37; Ziebell, Heiko 9; Lebas, Benedicte S. M. 1

1 Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium)
2 FERA Science Ltd, York Biotechnology Campus, Sand Hutton, York (United Kingdom)
3 Department of Plant Pathology, University of California-Davis, Davis, CA 95616 (USA)
4 Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke (Belgium)
5 Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON (Canada)
6 Institute for Agrifood Research Innovations (IAFRI), Newcastle University (United Kingdom)
7 Univ. Bordeaux, INRAE, UMR Biologie du Fruit et Pathologie, Villenave d’Ornon (France)
8 CRA-W, Walloon Agricultural Research Centre (Belgium)
9 Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony (Germany)
10 ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM (France)
11 Plant Health Diagnostic Laboratory, Ministry for Primary Industries (New Zealand)
12 USDA-APHIS, PPQ, Plant Germplasm and Quarantine Program (USA)
13 Bejo Zaden BV, Warmenhuizen, Noord-Holland (The Netherlands)
14 CGIAR, Consultative Group for International Agricultural Research
15 Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana (Slovenia)
16 Institute for Sustainable Agriculture, CSIC, Av. Menedez Pidal s/n, Campus Alameda del Obispo, 14004 Córdoba (Spain)
17 School of Natural Sciences, University of Tasmania (Australia)
18 USDA-APHIS, BRS, Biotechnology Risk Analysis Programs (USA)
19 Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, (South Africa)
20 Citrus Research International, PO Box 2201, Matieland, 7602 (South Africa)
21 Agriculture Victoria, AgriBio Centre for AgriBiosciences, 5 Ring Road, Bundoora, VIC 3083 (Australia)
22 School for Viticulture and Enology, University of Nova Gorica, Vipava (Slovenia)
23 IPSP-CNR, Institute for Sustainable Plant Protection, Consiglio Nazionale delle Ricerche, via Amendola 122/D, 70126 Bari (Italy)
24 USDA-ARS, Horticultural Crops Research Unit (USA)
25 Food and Agriculture Organization of the United Nations (FAO-UN), International Plant Protection Convention (IPPC)
26 USDA-APHIS, PPQ, Science and Technology (USA)
27 European and Mediterranean Plant Protection Organization, 21 Bd Richard Lenoir, 75011 Paris (France)
28 BeeOdiversity, Thines (Belgium)
29 Liverpool John Moores University, School of Biological and Environmental Sciences, Byrom Street, L33AF (United Kingdom)
30 Netherlands Food and Consumer Product Safety Authority, National Plant Protection Organization (the Netherlands)
31 Plant Analytics, Finnish Food Authority (Finland)
32 International Seed Federation, Chemin du Reposoir 7, 1260 Nyon (Switzerland)
33 Department of Agricultural, Forest and Food Sciences and AGROINNOVA – Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino (Italy)
34 Biosciences, University of Exeter, Exeter EX4 4QD (United Kingdom)
35 Wageningen University and Research, Wageningen (the Netherlands)
36 Instituto Nacional de Investigação Agrária e Veterinária (INIAV I.P.), Quinta do Marquês, Oeiras (Portugal)
37 DLR Rheinpfalz, Institute of Plant Protection, 67435 Neustadt an der Weinstrasse (Germany)
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {Massart, Sebastien and Adams, Ian and Al Rwahnih, Maher and Baeyen, Steve and Bilodeau, Guillaume J. and Blouin, Arnaud G. and Boonham, Neil and Candresse, Thierry and Chandellier, Anne and De Jonghe, Kris and Fox, Adrian and Gaafar, Yahya Z.A. and Gentit, Pascal and Haegeman, Annelies and Ho, Wellcome and Hurtado-Gonzales, Oscar and Jonkers, Wilfried and Kreuze, Jan and Kutjnak, Denis and Landa, Blanca B. and Liu, Mingxin and Maclot, Fran\c{c}ois and Malapi-Wight, Marta and Maree, Hans J. and Martoni, Francesco and Mehle, Natasa and Minafra, Angelantonio and Mollov, Dimitre and Moreira, Adriana G. and Nakhla, Mark and Petter, Fran\c{c}oise and Piper, Alexander M. and Ponchart, Julien P. and Rae, Robbie and Remenant, Benoit and Rivera, Yazmin and Rodoni, Brendan and Botermans, Marleen and Roenhorst, J.W. and Rollin, Johan and Saldarelli, Pasquale and Santala, Johanna and Souza-Richards, Rose and Spadaro, Davide and Studholme, David J. and Sultmanis, Stefanie and van der Vlugt, Ren\'e and Tamisier, Lucie and Trontin, Charlotte and Vazquez-Iglesias, Ines and Vicente, Claudia S.L. and van de Vossenberg, Bart T.L.H. and Westenberg, Marcel and Wetzel, Thierry and Ziebell, Heiko and Lebas, Benedicte S. M.},
     title = {Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests},
     journal = {Peer Community Journal},
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     publisher = {Peer Community In},
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Massart, Sebastien; Adams, Ian; Al Rwahnih, Maher; Baeyen, Steve; Bilodeau, Guillaume J.; Blouin, Arnaud G.; Boonham, Neil; Candresse, Thierry; Chandellier, Anne; De Jonghe, Kris; Fox, Adrian; Gaafar, Yahya Z.A.; Gentit, Pascal; Haegeman, Annelies; Ho, Wellcome; Hurtado-Gonzales, Oscar; Jonkers, Wilfried; Kreuze, Jan; Kutjnak, Denis; Landa, Blanca B.; Liu, Mingxin; Maclot, François; Malapi-Wight, Marta; Maree, Hans J.; Martoni, Francesco; Mehle, Natasa; Minafra, Angelantonio; Mollov, Dimitre; Moreira, Adriana G.; Nakhla, Mark; Petter, Françoise; Piper, Alexander M.; Ponchart, Julien P.; Rae, Robbie; Remenant, Benoit; Rivera, Yazmin; Rodoni, Brendan; Botermans, Marleen; Roenhorst, J.W.; Rollin, Johan; Saldarelli, Pasquale; Santala, Johanna; Souza-Richards, Rose; Spadaro, Davide; Studholme, David J.; Sultmanis, Stefanie; van der Vlugt, René; Tamisier, Lucie; Trontin, Charlotte; Vazquez-Iglesias, Ines; Vicente, Claudia S.L.; van de Vossenberg, Bart T.L.H.; Westenberg, Marcel; Wetzel, Thierry; Ziebell, Heiko; Lebas, Benedicte S. M. Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests. Peer Community Journal, Volume 2 (2022), article  no. e62. doi : 10.24072/pcjournal.181.

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.infections.100002

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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