Section: Infections
Topic:
Biology of interactions,
Plant biology,
Genetics/Genomics
Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests
Corresponding author(s): Massart, Sebastien (sebastien.massart@uliege.be)
10.24072/pcjournal.181 - Peer Community Journal, Volume 2 (2022), article no. e62.
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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.
Type: Opinion / perspective
Massart, Sebastien 1; Adams, Ian 2; Al Rwahnih, Maher 3; Baeyen, Steve 4; Bilodeau, Guillaume J. 5; Blouin, Arnaud G. 1; Boonham, Neil 6; Candresse, Thierry 7; Chandellier, Anne 8; De Jonghe, Kris 4; Fox, Adrian 2; Gaafar, Yahya Z.A. 9; Gentit, Pascal 10; Haegeman, Annelies 4; Ho, Wellcome 11; Hurtado-Gonzales, Oscar 12; Jonkers, Wilfried 13; Kreuze, Jan 14; Kutjnak, Denis 15; Landa, Blanca B. 16; Liu, Mingxin 17; Maclot, François 1; Malapi-Wight, Marta 18; Maree, Hans J. 19, 20; Martoni, Francesco 21; Mehle, Natasa 15, 22; Minafra, Angelantonio 23; Mollov, Dimitre 24; Moreira, Adriana G. 25; Nakhla, Mark 26; Petter, Françoise 27; Piper, Alexander M. 21; Ponchart, Julien P. 1, 28; Rae, Robbie 29; Remenant, Benoit 10; Rivera, Yazmin 26; Rodoni, Brendan 21; Botermans, Marleen 30; Roenhorst, J.W. 30; Rollin, Johan 1; Saldarelli, Pasquale 23; Santala, Johanna 31; Souza-Richards, Rose 32; Spadaro, Davide 33; Studholme, David J. 34; Sultmanis, Stefanie 5; van der Vlugt, René 35; Tamisier, Lucie 1; Trontin, Charlotte 27; Vazquez-Iglesias, Ines 2; Vicente, Claudia S.L. 36; van de Vossenberg, Bart T.L.H. 30; Westenberg, Marcel 30; Wetzel, Thierry 37; Ziebell, Heiko 9; Lebas, Benedicte S. M. 1
CC-BY 4.0
@article{10_24072_pcjournal_181,
author = {Massart, Sebastien and Adams, Ian and Al Rwahnih, Maher and Baeyen, Steve and Bilodeau, Guillaume J. and Blouin, Arnaud G. and Boonham, Neil and Candresse, Thierry and Chandellier, Anne and De Jonghe, Kris and Fox, Adrian and Gaafar, Yahya Z.A. and Gentit, Pascal and Haegeman, Annelies and Ho, Wellcome and Hurtado-Gonzales, Oscar and Jonkers, Wilfried and Kreuze, Jan and Kutjnak, Denis and Landa, Blanca B. and Liu, Mingxin and Maclot, Fran\c{c}ois and Malapi-Wight, Marta and Maree, Hans J. and Martoni, Francesco and Mehle, Natasa and Minafra, Angelantonio and Mollov, Dimitre and Moreira, Adriana G. and Nakhla, Mark and Petter, Fran\c{c}oise and Piper, Alexander M. and Ponchart, Julien P. and Rae, Robbie and Remenant, Benoit and Rivera, Yazmin and Rodoni, Brendan and Botermans, Marleen and Roenhorst, J.W. and Rollin, Johan and Saldarelli, Pasquale and Santala, Johanna and Souza-Richards, Rose and Spadaro, Davide and Studholme, David J. and Sultmanis, Stefanie and van der Vlugt, Ren\'e and Tamisier, Lucie and Trontin, Charlotte and Vazquez-Iglesias, Ines and Vicente, Claudia S.L. and van de Vossenberg, Bart T.L.H. and Westenberg, Marcel and Wetzel, Thierry and Ziebell, Heiko and Lebas, Benedicte S. M.},
title = {Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests},
journal = {Peer Community Journal},
eid = {e62},
publisher = {Peer Community In},
volume = {2},
year = {2022},
doi = {10.24072/pcjournal.181},
url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.181/}
}
TY - JOUR AU - Massart, Sebastien AU - Adams, Ian AU - Al Rwahnih, Maher AU - Baeyen, Steve AU - Bilodeau, Guillaume J. AU - Blouin, Arnaud G. AU - Boonham, Neil AU - Candresse, Thierry AU - Chandellier, Anne AU - De Jonghe, Kris AU - Fox, Adrian AU - Gaafar, Yahya Z.A. AU - Gentit, Pascal AU - Haegeman, Annelies AU - Ho, Wellcome AU - Hurtado-Gonzales, Oscar AU - Jonkers, Wilfried AU - Kreuze, Jan AU - Kutjnak, Denis AU - Landa, Blanca B. AU - Liu, Mingxin AU - Maclot, François AU - Malapi-Wight, Marta AU - Maree, Hans J. AU - Martoni, Francesco AU - Mehle, Natasa AU - Minafra, Angelantonio AU - Mollov, Dimitre AU - Moreira, Adriana G. AU - Nakhla, Mark AU - Petter, Françoise AU - Piper, Alexander M. AU - Ponchart, Julien P. AU - Rae, Robbie AU - Remenant, Benoit AU - Rivera, Yazmin AU - Rodoni, Brendan AU - Botermans, Marleen AU - Roenhorst, J.W. AU - Rollin, Johan AU - Saldarelli, Pasquale AU - Santala, Johanna AU - Souza-Richards, Rose AU - Spadaro, Davide AU - Studholme, David J. AU - Sultmanis, Stefanie AU - van der Vlugt, René AU - Tamisier, Lucie AU - Trontin, Charlotte AU - Vazquez-Iglesias, Ines AU - Vicente, Claudia S.L. AU - van de Vossenberg, Bart T.L.H. AU - Westenberg, Marcel AU - Wetzel, Thierry AU - Ziebell, Heiko AU - Lebas, Benedicte S. M. TI - Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests JO - Peer Community Journal PY - 2022 VL - 2 PB - Peer Community In UR - https://peercommunityjournal.org/articles/10.24072/pcjournal.181/ DO - 10.24072/pcjournal.181 ID - 10_24072_pcjournal_181 ER -
%0 Journal Article %A Massart, Sebastien %A Adams, Ian %A Al Rwahnih, Maher %A Baeyen, Steve %A Bilodeau, Guillaume J. %A Blouin, Arnaud G. %A Boonham, Neil %A Candresse, Thierry %A Chandellier, Anne %A De Jonghe, Kris %A Fox, Adrian %A Gaafar, Yahya Z.A. %A Gentit, Pascal %A Haegeman, Annelies %A Ho, Wellcome %A Hurtado-Gonzales, Oscar %A Jonkers, Wilfried %A Kreuze, Jan %A Kutjnak, Denis %A Landa, Blanca B. %A Liu, Mingxin %A Maclot, François %A Malapi-Wight, Marta %A Maree, Hans J. %A Martoni, Francesco %A Mehle, Natasa %A Minafra, Angelantonio %A Mollov, Dimitre %A Moreira, Adriana G. %A Nakhla, Mark %A Petter, Françoise %A Piper, Alexander M. %A Ponchart, Julien P. %A Rae, Robbie %A Remenant, Benoit %A Rivera, Yazmin %A Rodoni, Brendan %A Botermans, Marleen %A Roenhorst, J.W. %A Rollin, Johan %A Saldarelli, Pasquale %A Santala, Johanna %A Souza-Richards, Rose %A Spadaro, Davide %A Studholme, David J. %A Sultmanis, Stefanie %A van der Vlugt, René %A Tamisier, Lucie %A Trontin, Charlotte %A Vazquez-Iglesias, Ines %A Vicente, Claudia S.L. %A van de Vossenberg, Bart T.L.H. %A Westenberg, Marcel %A Wetzel, Thierry %A Ziebell, Heiko %A Lebas, Benedicte S. M. %T Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests %J Peer Community Journal %D 2022 %V 2 %I Peer Community In %U https://peercommunityjournal.org/articles/10.24072/pcjournal.181/ %R 10.24072/pcjournal.181 %F 10_24072_pcjournal_181
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, Volume 2 (2022), article no. e62. doi : 10.24072/pcjournal.181. https://peercommunityjournal.org/articles/10.24072/pcjournal.181/
PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.infections.100002
Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.
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