PCI Infections

Title *

Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pestsuse asterix (*) to get italics

Authors *

S. Massart, I. Adams, M. Al Rwahnih, S. Baeyen, G. J. Bilodeau, A. G. Blouin, N. Boonham, T. Candresse, A. Chandelier, K. De Jonghe, A. Fox, Y.Z.A. Gaafar, P. Gentit, A. Haegeman, W. Ho, O. Hurtado-Gonzales, W. Jonkers, J. Kreuze, D. Kutjnak, B. B. Landa, M. Liu, F. Maclot, M. Malapi-Wight, H. J. Maree, F. Martoni, N. Mehle, A. Minafra, D. Mollov, A. G. Moreira, M. Nakhla, F. Petter, A.M. Piper, J. P. Ponchart, R. Rae, B. Remenant, Y. Rivera, B. Rodoni, M. Botermans, J.W. Roenhorst, J. Rollin , P. Saldarelli, J. Santala, R. Souza-Richards, D. Spadaro, D. J. Studholme, S. Sultmanis, R. van der Vlugt, L. Tamisier, C. Trontin, I. Vazquez-Iglesias, C. S. L. Vicente, B. T. L. H. van de Vossenberg, M. Westenberg, T. Wetzel, H. Ziebell and B. S. M. Lebas Please use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2022

Picture *

Abstract *

<p style="text-align: justify;">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.</p> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div>

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Keywords (optional)

detection, high htroughput sequencing, plant pest, plant pathogen

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Diagnosis, Pest management, Phytopathology, Plant diseases

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Submission date

2022-06-13 11:26:18

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Olivier Schumpp

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