Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description
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 developmen...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/141987 |
| _version_ | 1855532705043709952 |
|---|---|
| author | Lebas, B. Adams, I. Rwahnih, M.A. Baeyen, S. Bilodeau, G.J. Blouin, A.G. Boonham, N. Candresse, T. Chandelier, A. Jonghe, K. de Fox, A. Gaafar, Y.Z.A. Gentit, P. Haegeman, A. Ho, W. Hurtado-Gonzales, O. Jonkers, W. Kreuze, Jan F. Kutjnak, D. Landa, B. Liu, M. Maclot, F. Malapi-Wight, M. Maree, H.J. Martoni, F. Mehle, N. Minafra, A. Mollov, D. Moreira, A. Nakhla, M. Petter, F. Piper, A.M. Ponchart, J. Rae, R. Remenant, B. Rivera, Y. Rodoni, B. Roenhorst, J.W. Rollin, J. Saldarelli, P. Santala, J. Souza-Richards, R. Spadaro, D. Studholme, D. Sultmanis, S. Vlugt, R. van der. Tamisier, L. Trontin, C. Vazquez-Iglesias, I. Vicente, C.S.L. Vossenberg, B.T.L.H. Wetzel, T. Ziebell, H. Massart, S. |
| author_browse | Adams, I. Baeyen, S. Bilodeau, G.J. Blouin, A.G. Boonham, N. Candresse, T. Chandelier, A. Fox, A. Gaafar, Y.Z.A. Gentit, P. Haegeman, A. Ho, W. Hurtado-Gonzales, O. Jonghe, K. de Jonkers, W. Kreuze, Jan F. Kutjnak, D. Landa, B. Lebas, B. Liu, M. Maclot, F. Malapi-Wight, M. Maree, H.J. Martoni, F. Massart, S. Mehle, N. Minafra, A. Mollov, D. Moreira, A. Nakhla, M. Petter, F. Piper, A.M. Ponchart, J. Rae, R. Remenant, B. Rivera, Y. Rodoni, B. Roenhorst, J.W. Rollin, J. Rwahnih, M.A. Saldarelli, P. Santala, J. Souza-Richards, R. Spadaro, D. Studholme, D. Sultmanis, S. Tamisier, L. Trontin, C. Vazquez-Iglesias, I. Vicente, C.S.L. Vlugt, R. van der. Vossenberg, B.T.L.H. Wetzel, T. Ziebell, H. |
| author_facet | Lebas, B. Adams, I. Rwahnih, M.A. Baeyen, S. Bilodeau, G.J. Blouin, A.G. Boonham, N. Candresse, T. Chandelier, A. Jonghe, K. de Fox, A. Gaafar, Y.Z.A. Gentit, P. Haegeman, A. Ho, W. Hurtado-Gonzales, O. Jonkers, W. Kreuze, Jan F. Kutjnak, D. Landa, B. Liu, M. Maclot, F. Malapi-Wight, M. Maree, H.J. Martoni, F. Mehle, N. Minafra, A. Mollov, D. Moreira, A. Nakhla, M. Petter, F. Piper, A.M. Ponchart, J. Rae, R. Remenant, B. Rivera, Y. Rodoni, B. Roenhorst, J.W. Rollin, J. Saldarelli, P. Santala, J. Souza-Richards, R. Spadaro, D. Studholme, D. Sultmanis, S. Vlugt, R. van der. Tamisier, L. Trontin, C. Vazquez-Iglesias, I. Vicente, C.S.L. Vossenberg, B.T.L.H. Wetzel, T. Ziebell, H. Massart, S. |
| author_sort | Lebas, B. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace141987 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1419872025-12-08T09:54:28Z Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description Lebas, B. Adams, I. Rwahnih, M.A. Baeyen, S. Bilodeau, G.J. Blouin, A.G. Boonham, N. Candresse, T. Chandelier, A. Jonghe, K. de Fox, A. Gaafar, Y.Z.A. Gentit, P. Haegeman, A. Ho, W. Hurtado-Gonzales, O. Jonkers, W. Kreuze, Jan F. Kutjnak, D. Landa, B. Liu, M. Maclot, F. Malapi-Wight, M. Maree, H.J. Martoni, F. Mehle, N. Minafra, A. Mollov, D. Moreira, A. Nakhla, M. Petter, F. Piper, A.M. Ponchart, J. Rae, R. Remenant, B. Rivera, Y. Rodoni, B. Roenhorst, J.W. Rollin, J. Saldarelli, P. Santala, J. Souza-Richards, R. Spadaro, D. Studholme, D. Sultmanis, S. Vlugt, R. van der. Tamisier, L. Trontin, C. Vazquez-Iglesias, I. Vicente, C.S.L. Vossenberg, B.T.L.H. Wetzel, T. Ziebell, H. Massart, S. high-throughput sequencing plant pests 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. 2022-08 2024-05-21T18:22:47Z 2024-05-21T18:22:47Z Journal Article https://hdl.handle.net/10568/141987 en Open Access Wiley Lebas, B.; Adams, I.; Rwahnih, M.A.; Baeyen, S.; Bilodeau, G.J.; Blouin, A.G.; Boonham, N.; Candresse, T.; Chandelier, A.; De Jonghe, K.; Fox, A.; Gaafar, Y.Z.A.; Gentit, P.; Haegeman, A.; Ho, W.; Hurtado‐Gonzales, O.; Jonkers, W.; Kreuze, J.; Kutjnak, D.; Landa, B.; Liu, M.; Maclot, F.; Malapi-Wight, M.; Maree, H.J.; Martoni, F.; Mehle, N.; Minafra, A.; Mollov, D.; Moreira, A.; Nakhla, M.; Petter, F.; Piper, A.M.; Ponchart, J.; Rae, R.; Remenant, B.; Rivera, Y.; Rodoni, B.; Roenhorst, J.W.; Rollin, J.; Saldarelli, P.; Santala, J.; Souza-Richards, R.; Spadaro, D.; Studholme, D.; Sultmanis, S.; Vlugt, R. van der; Tamisier, L.; Trontin, C.; Vazquez-Iglesias, I.; Vicente, C.S.L.; Vossenberg, B.T.L.H.; Wetzel, T.; Ziebell, H.; Massart, S. 2022. Facilitating the adoption of high‐throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step‐by‐step description. Bulletin OEPP. ISSN 1365-2338. 52(2), 394–418. https://doi.org/10.1111/epp.12863 |
| spellingShingle | high-throughput sequencing plant pests Lebas, B. Adams, I. Rwahnih, M.A. Baeyen, S. Bilodeau, G.J. Blouin, A.G. Boonham, N. Candresse, T. Chandelier, A. Jonghe, K. de Fox, A. Gaafar, Y.Z.A. Gentit, P. Haegeman, A. Ho, W. Hurtado-Gonzales, O. Jonkers, W. Kreuze, Jan F. Kutjnak, D. Landa, B. Liu, M. Maclot, F. Malapi-Wight, M. Maree, H.J. Martoni, F. Mehle, N. Minafra, A. Mollov, D. Moreira, A. Nakhla, M. Petter, F. Piper, A.M. Ponchart, J. Rae, R. Remenant, B. Rivera, Y. Rodoni, B. Roenhorst, J.W. Rollin, J. Saldarelli, P. Santala, J. Souza-Richards, R. Spadaro, D. Studholme, D. Sultmanis, S. Vlugt, R. van der. Tamisier, L. Trontin, C. Vazquez-Iglesias, I. Vicente, C.S.L. Vossenberg, B.T.L.H. Wetzel, T. Ziebell, H. Massart, S. Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description |
| title | Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description |
| title_full | Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description |
| title_fullStr | Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description |
| title_full_unstemmed | Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description |
| title_short | Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description |
| title_sort | facilitating the adoption of high throughput sequencing technologies as a plant pest diagnostic test in laboratories a step by step description |
| topic | high-throughput sequencing plant pests |
| url | https://hdl.handle.net/10568/141987 |
| work_keys_str_mv | AT lebasb facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT adamsi facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT rwahnihma facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT baeyens facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT bilodeaugj facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT blouinag facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT boonhamn facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT candresset facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT chandeliera facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT jonghekde facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT foxa facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT gaafaryza facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT gentitp facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT haegemana facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT how facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT hurtadogonzaleso facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT jonkersw facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT kreuzejanf facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT kutjnakd facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT landab facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT lium facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT maclotf facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT malapiwightm facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT mareehj facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT martonif facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT mehlen facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT minafraa facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT mollovd facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT moreiraa facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT nakhlam facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT petterf facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT piperam facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT ponchartj facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT raer facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT remenantb facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT riveray facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT rodonib facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT roenhorstjw facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT rollinj facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT saldarellip facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT santalaj facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT souzarichardsr facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT spadarod facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT studholmed facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT sultmaniss facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT vlugtrvander facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT tamisierl facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT trontinc facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT vazqueziglesiasi facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT vicentecsl facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT vossenbergbtlh facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT wetzelt facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT ziebellh facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription AT massarts facilitatingtheadoptionofhighthroughputsequencingtechnologiesasaplantpestdiagnostictestinlaboratoriesastepbystepdescription |