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>

Indicate the full web address (DOI or URL) giving public access to these data (if you have any problems with the deposit of your data, please contact contact@infections.peercommunityin.org). In case all raw data are included in the preprint, indicate the DOI or URL of the preprint.

You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

Indicate the full web address (DOI or URL) giving public access to these scripts (if you have any problems with the deposit of your scripts, please contact contact@infections.peercommunityin.org). In case all raw scripts are included in the preprint, indicate the DOI or URL of the preprint.

You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@infections.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint.

You should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Keywords

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

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

No need for them to be recommenders of PCIInfections. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

Opposed reviewers - Suggest up to 5 people not to invite as reviewers. (Optional)

e.g. John Doe [john@doe.com]

Submission date

2022-06-13 11:26:18

Recommender

Olivier Schumpp

Reviewers

or Register
Submit a preprint

MANAGING BOARD

MEMBER OF

INDEXED BY