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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #395616
Research Project: Development of Knowledge-based Approaches for Disease Management in Small Fruit and Nursery Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

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

Author
item MASSART, SEBASTIAN - UNIVERSITY OF LIEGE
item ADAMS, IAN - FERA SCIENCE LTD.
item AL RWAHNIH, MAHER - UNIVERSITY OF CALIFORNIA, DAVIS
item BAEYEN, STEVE - FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE
item BILODEAU, GUILLAUME - CANADIAN FOOD INSPECTION AGENCY
item BLOUIN, ARNAUD - UNIVERSITY OF LIEGE
item BOONHAM, NEIL - UNIVERSITY OF NEWCASTLE
item CANDRESSE, THIERRY - FRENCH NATIONAL INSTITUTE FOR AGRICULTURAL RESEARCH
item CHANDELIER, ANNE - WALLOON AGRICULTURAL RESEARCH CENTER
item DE JONGHE, KRIS - FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE
item FOX, ADRIAN - FERA SCIENCE LTD.
item GAAFAR, YAHYA - JULIUS KUHN INSTITUTE
item GENTIT, PASCAL - FRENCH AGENCY FOR FOOD, ENVIRONMENTAL AND OCCUPATIONAL HEALTH & SAFETY (ANSES)
item HAEGEMAN, ANNELIES - FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE
item HO, WELLCOME - MINISTRY FOR PRIMARY INDUSTRIES
item HURTADO-GONZALES, OSCAR
item KREUZE, JAN - INTERNATIONAL POTATO CENTER
item KUTJNAK, DENIS - NATIONAL INSTITUTE OF BIOLOGY
item LANDA, BLANCA - INSTITUTO DE AGRICULTURA
item LIU, MINGXIN - UNIVERSITY OF TASMANIA
item MACLOT, FRANCOIS - UNIVERSITY OF LIEGE
item WIGHT-MALAPI, MARTHA
item MAREE, HANO - STELLENBOSCH UNIVERSITY
item MARTONI, FRANCESCO - AGRICULTURE RESEARCH AND DEVELOPMENT, DEPARTMENT OF ECONOMIC DEVELOPMENT, JOBS, TRANSPORT AND RESOURCES
item MEHLE, NATASA - NATIONAL INSTITUTE OF BIOLOGY
item MINAFRA, ANGELANTONIO - INSTITUTE FOR SUSTAINABLE AGRICULTURE
item MOLLOV, DIMITRE
item MOREIRA, ADRIANA - FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS (FAO)
item NAKHLA, MARK - ANIMAL AND PLANT HEALTH INSPECTION SERVICE (APHIS)
item PETTER, FRANCOISE - EUROPEAN AND MEDITERRANEAN PLANT PROTECTION ORGANIZATION(EPPO)
item PIPER, ALEXANDER - FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE
item PONCHART, JULIEN - BEEODIVERSITY
item RAE, ROBBIE - LIVERPOOL JOHN MOORES UNIVERSITY
item REMENANT, BENOIT - FRENCH AGENCY FOR FOOD, ENVIRONMENTAL AND OCCUPATIONAL HEALTH & SAFETY (ANSES)
item RIVERA, YAZMIN
item RODONI, BRENDAN - AGRICULTURE VICTORIA
item BOTERMANS, MARLEEN - NETHERLANDS FOOD AND CONSUMER PRODUCTION SAFETY AUTHORITY(NVWA)
item ROENHORST, ANNELIEN - NETHERLANDS FOOD AND CONSUMER PRODUCTION SAFETY AUTHORITY(NVWA)
item ROLLIN, JOHAN - UNIVERSITY OF LIEGE
item SALDARELLI, PASQUALE - INSTITUTE FOR SUSTAINABLE AGRICULTURE
item SANTALA, JOHANNA - FINNISH FOOD SAFETY AUTHORITY
item SPADARO, DAVIDE - UNIVERSITY OF TURIN
item SOUZA-RICHARDS, ROSA - INTERNATIONAL SEED FEDERATION
item STUDHOLME, DAVID - UNIVERSITY OF EXETER
item SULTIMANIS, STEFANIE - INNOVATION, SCIENCE AND ECONOMIC DEVELOPMENT CANADA
item VAN DER VLUGT, RENE - WAGENINGEN UNIVERSITY
item TAMISIER, LUCIE - UNIVERSITY OF LIEGE
item TRONTIN, CHARLOTTE - EUROPEAN AND MEDITERRANEAN PLANT PROTECTION ORGANIZATION(EPPO)
item VAZQUEZ-IGLESIAS, INES - FERA SCIENCE LTD.
item VICENTE, CLAUDIA - INSTITUTO NACIONAL DE INVESTIGAÇÃO AGRÁRIA E VETERINÁRIA
item VOSSENBERG, BART VAN DE - NETHERLANDS FOOD AND CONSUMER PRODUCTION SAFETY AUTHORITY(NVWA)
item WESTENBERG, MARCEL - NETHERLANDS FOOD AND CONSUMER PRODUCTION SAFETY AUTHORITY(NVWA)
item WETZEL, THIERRY - INSTITUTE FOR PLANT PROTECTION IN FIELD CROPS AND GRASSLAND
item ZIEBELL, HEIKO - JULIUS KUHN INSTITUTE
item LEBAS, BENEDICTE - UNIVERSITY OF LIEGE

Submitted to: Review Article
Publication Type: Review Article
Publication Acceptance Date: 9/30/2022
Publication Date: 10/25/2022
Citation: Massart, S., Adams, I., Al Rwahnih, M., Baeyen, S., Bilodeau, G., Blouin, A., Boonham, N., Candresse, T., Chandelier, A., De Jonghe, K., Fox, A., Gaafar, Y., Gentit, P., Haegeman, A., Ho, W., Hurtado-Gonzales, O.P., Kreuze, J., Kutjnak, D., Landa, B., Liu, M., Maclot, F., Wight-Malapi, M., Maree, H., Martoni, F., Mehle, N., Minafra, A., Mollov, D.S., Moreira, A., Nakhla, M., Petter, F., Piper, A., Ponchart, J., Rae, R., Remenant, B., Rivera, Y., Rodoni, B., Botermans, M., Roenhorst, A., Rollin, J., Saldarelli, P., Santala, J., Spadaro, D., Souza-Richards, R., Studholme, D., Sultimanis, S., Van Der Vlugt, R., Tamisier, L., Trontin, C., Vazquez-Iglesias, I., Vicente, C., Vossenberg, B., Westenberg, M., Wetzel, T., Ziebell, H., Lebas, B. 2022. Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests. Review Article. volume 2, article e62. https://doi.org/10.24072/pcjournal.181.
DOI: https://doi.org/10.24072/pcjournal.181

Interpretive Summary: High-throughput sequencing (HTS) is the most advanced diagnostic technology for plant pests and pathogens. However, HTS is the most complex diagnostics method. The review points addressed here are on risk analysis, reference materials, use of positive and negative controls, and validation. Specifity, selectivity, and reproducibility of HTS data and its use for diagnostics and regulatory purposes is widely discussed. These recommendations provided here on using HTS as a diagnostic test can be applied for the detection and identification of any plant pest by plant health diagnostic laboratories serving diagnostics, industry, or regulatory entities.

Technical Abstract: 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, mycetes, 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.