Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests
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 ro...
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| Format: | Article |
| Language: | English |
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Peer Community In
2022-10-01
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| Series: | Peer Community Journal |
| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.181/ |
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| author | 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. |
| author_facet | 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. |
| author_sort | Massart, Sebastien |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T16:11:11Z |
| format | Article |
| id | doaj.art-6b2f4495a4ed47ba995a8336341967a7 |
| institution | Directory Open Access Journal |
| issn | 2804-3871 |
| language | English |
| last_indexed | 2024-03-11T16:11:11Z |
| publishDate | 2022-10-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj.art-6b2f4495a4ed47ba995a8336341967a72023-10-24T14:38:35ZengPeer Community InPeer Community Journal2804-38712022-10-01210.24072/pcjournal.18110.24072/pcjournal.181Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pestsMassart, Sebastien0Adams, Ian1Al Rwahnih, Maher2Baeyen, Steve3Bilodeau, Guillaume J.4Blouin, Arnaud G.5Boonham, Neil6Candresse, Thierry7Chandellier, Anne8De Jonghe, Kris9Fox, Adrian10Gaafar, Yahya Z.A.11Gentit, Pascal12Haegeman, Annelies13Ho, Wellcome14Hurtado-Gonzales, Oscar15Jonkers, Wilfried16Kreuze, Jan17Kutjnak, Denis18Landa, Blanca B.19Liu, Mingxin20Maclot, François21Malapi-Wight, Marta22Maree, Hans J.23Martoni, Francesco24Mehle, Natasa25Minafra, Angelantonio26Mollov, Dimitre27Moreira, Adriana G.28Nakhla, Mark29Petter, Françoise30Piper, Alexander M.31Ponchart, Julien P.32Rae, Robbie33Remenant, Benoit34Rivera, Yazmin35Rodoni, Brendan36Botermans, Marleen37Roenhorst, J.W.38Rollin, Johan39Saldarelli, Pasquale40Santala, Johanna41Souza-Richards, Rose42Spadaro, Davide43Studholme, David J.44Sultmanis, Stefanie45van der Vlugt, René46Tamisier, Lucie47Trontin, Charlotte48Vazquez-Iglesias, Ines49Vicente, Claudia S.L.50van de Vossenberg, Bart T.L.H.51Westenberg, Marcel52Wetzel, Thierry53Ziebell, Heiko54Lebas, Benedicte S. M.55Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium)FERA Science Ltd, York Biotechnology Campus, Sand Hutton, York (United Kingdom)Department of Plant Pathology, University of California-Davis, Davis, CA 95616 (USA)Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke (Belgium)Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON (Canada)Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium)Institute for Agrifood Research Innovations (IAFRI), Newcastle University (United Kingdom)Univ. Bordeaux, INRAE, UMR Biologie du Fruit et Pathologie, Villenave d’Ornon (France)CRA-W, Walloon Agricultural Research Centre (Belgium)Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke (Belgium)FERA Science Ltd, York Biotechnology Campus, Sand Hutton, York (United Kingdom)Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony (Germany)ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM (France)Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke (Belgium)Plant Health Diagnostic Laboratory, Ministry for Primary Industries (New Zealand)USDA-APHIS, PPQ, Plant Germplasm and Quarantine Program (USA)Bejo Zaden BV, Warmenhuizen, Noord-Holland (The Netherlands)CGIAR, Consultative Group for International Agricultural ResearchDepartment of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana (Slovenia)Institute for Sustainable Agriculture, CSIC, Av. Menedez Pidal s/n, Campus Alameda del Obispo, 14004 Córdoba (Spain)School of Natural Sciences, University of Tasmania (Australia)Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium)USDA-APHIS, BRS, Biotechnology Risk Analysis Programs (USA)Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, (South Africa); Citrus Research International, PO Box 2201, Matieland, 7602 (South Africa)Agriculture Victoria, AgriBio Centre for AgriBiosciences, 5 Ring Road, Bundoora, VIC 3083 (Australia)Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana (Slovenia); School for Viticulture and Enology, University of Nova Gorica, Vipava (Slovenia)IPSP-CNR, Institute for Sustainable Plant Protection, Consiglio Nazionale delle Ricerche, via Amendola 122/D, 70126 Bari (Italy)USDA-ARS, Horticultural Crops Research Unit (USA)Food and Agriculture Organization of the United Nations (FAO-UN), International Plant Protection Convention (IPPC)USDA-APHIS, PPQ, Science and Technology (USA)European and Mediterranean Plant Protection Organization, 21 Bd Richard Lenoir, 75011 Paris (France)Agriculture Victoria, AgriBio Centre for AgriBiosciences, 5 Ring Road, Bundoora, VIC 3083 (Australia)Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium); BeeOdiversity, Thines (Belgium)Liverpool John Moores University, School of Biological and Environmental Sciences, Byrom Street, L33AF (United Kingdom)ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM (France)USDA-APHIS, PPQ, Science and Technology (USA)Agriculture Victoria, AgriBio Centre for AgriBiosciences, 5 Ring Road, Bundoora, VIC 3083 (Australia)Netherlands Food and Consumer Product Safety Authority, National Plant Protection Organization (the Netherlands)Netherlands Food and Consumer Product Safety Authority, National Plant Protection Organization (the Netherlands)Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium)IPSP-CNR, Institute for Sustainable Plant Protection, Consiglio Nazionale delle Ricerche, via Amendola 122/D, 70126 Bari (Italy)Plant Analytics, Finnish Food Authority (Finland)International Seed Federation, Chemin du Reposoir 7, 1260 Nyon (Switzerland)Department of Agricultural, Forest and Food Sciences and AGROINNOVA – Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino (Italy)Biosciences, University of Exeter, Exeter EX4 4QD (United Kingdom)Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON (Canada)Wageningen University and Research, Wageningen (the Netherlands)Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium)European and Mediterranean Plant Protection Organization, 21 Bd Richard Lenoir, 75011 Paris (France)FERA Science Ltd, York Biotechnology Campus, Sand Hutton, York (United Kingdom)Instituto Nacional de Investigação Agrária e Veterinária (INIAV I.P.), Quinta do Marquês, Oeiras (Portugal)Netherlands Food and Consumer Product Safety Authority, National Plant Protection Organization (the Netherlands)Netherlands Food and Consumer Product Safety Authority, National Plant Protection Organization (the Netherlands)DLR Rheinpfalz, Institute of Plant Protection, 67435 Neustadt an der Weinstrasse (Germany)Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony (Germany)Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium)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.https://peercommunityjournal.org/articles/10.24072/pcjournal.181/ |
| spellingShingle | 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 |
| title | Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests |
| title_full | Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests |
| title_fullStr | Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests |
| title_full_unstemmed | Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests |
| title_short | Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests |
| title_sort | guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.181/ |
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