Infections

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

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.

Published online:
DOI: 10.24072/pcjournal.181
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

1 Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège (Belgium)
2 FERA Science Ltd, York Biotechnology Campus, Sand Hutton, York (United Kingdom)
3 Department of Plant Pathology, University of California-Davis, Davis, CA 95616 (USA)
4 Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke (Belgium)
5 Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON (Canada)
6 Institute for Agrifood Research Innovations (IAFRI), Newcastle University (United Kingdom)
7 Univ. Bordeaux, INRAE, UMR Biologie du Fruit et Pathologie, Villenave d’Ornon (France)
8 CRA-W, Walloon Agricultural Research Centre (Belgium)
9 Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony (Germany)
10 ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM (France)
11 Plant Health Diagnostic Laboratory, Ministry for Primary Industries (New Zealand)
12 USDA-APHIS, PPQ, Plant Germplasm and Quarantine Program (USA)
13 Bejo Zaden BV, Warmenhuizen, Noord-Holland (The Netherlands)
14 CGIAR, Consultative Group for International Agricultural Research
15 Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana (Slovenia)
16 Institute for Sustainable Agriculture, CSIC, Av. Menedez Pidal s/n, Campus Alameda del Obispo, 14004 Córdoba (Spain)
17 School of Natural Sciences, University of Tasmania (Australia)
18 USDA-APHIS, BRS, Biotechnology Risk Analysis Programs (USA)
19 Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, (South Africa)
20 Citrus Research International, PO Box 2201, Matieland, 7602 (South Africa)
21 Agriculture Victoria, AgriBio Centre for AgriBiosciences, 5 Ring Road, Bundoora, VIC 3083 (Australia)
22 School for Viticulture and Enology, University of Nova Gorica, Vipava (Slovenia)
23 IPSP-CNR, Institute for Sustainable Plant Protection, Consiglio Nazionale delle Ricerche, via Amendola 122/D, 70126 Bari (Italy)
24 USDA-ARS, Horticultural Crops Research Unit (USA)
25 Food and Agriculture Organization of the United Nations (FAO-UN), International Plant Protection Convention (IPPC)
26 USDA-APHIS, PPQ, Science and Technology (USA)
27 European and Mediterranean Plant Protection Organization, 21 Bd Richard Lenoir, 75011 Paris (France)
28 BeeOdiversity, Thines (Belgium)
29 Liverpool John Moores University, School of Biological and Environmental Sciences, Byrom Street, L33AF (United Kingdom)
30 Netherlands Food and Consumer Product Safety Authority, National Plant Protection Organization (the Netherlands)
31 Plant Analytics, Finnish Food Authority (Finland)
32 International Seed Federation, Chemin du Reposoir 7, 1260 Nyon (Switzerland)
33 Department of Agricultural, Forest and Food Sciences and AGROINNOVA – Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino (Italy)
34 Biosciences, University of Exeter, Exeter EX4 4QD (United Kingdom)
35 Wageningen University and Research, Wageningen (the Netherlands)
36 Instituto Nacional de Investigação Agrária e Veterinária (INIAV I.P.), Quinta do Marquês, Oeiras (Portugal)
37 DLR Rheinpfalz, Institute of Plant Protection, 67435 Neustadt an der Weinstrasse (Germany)
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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     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},
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     publisher = {Peer Community In},
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     year = {2022},
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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/

Peer reviewed and recommended by PCI : 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.

[1] Adams, I. P.; Fox, A.; Boonham, N.; Massart, S.; De Jonghe, K. The impact of high throughput sequencing on plant health diagnostics, European Journal of Plant Pathology, Volume 152 (2018) no. 4, pp. 909-919 | DOI

[2] Adams, I. P.; Skelton, A.; Macarthur, R.; Hodges, T.; Hinds, H.; Flint, L.; Nath, P. D.; Boonham, N.; Fox, A. Carrot yellow leaf virus Is Associated with Carrot Internal Necrosis, PLoS ONE, Volume 9 (2014) no. 11 | DOI

[3] Aguayo, J.; Fourrier-Jeandel, C.; Husson, C.; Ioos, R. Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities, Applied and Environmental Microbiology, Volume 84 (2018) no. 11 | DOI

[4] Al Rwahnih, M.; Daubert, S.; Úrbez-Torres, J. R.; Cordero, F.; Rowhani, A. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses, Archives of Virology, Volume 156 (2011) no. 3, pp. 397-403 | DOI

[5] Aziz, N.; Zhao, Q.; Bry, L.; Driscoll, D. K.; Funke, B.; Gibson, J. S.; Grody, W. W.; Hegde, M. R.; Hoeltge, G. A.; Leonard, D. G. B.; Merker, J. D.; Nagarajan, R.; Palicki, L. A.; Robetorye, R. S.; Schrijver, I.; Weck, K. E.; Voelkerding, K. V. College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests, Archives of Pathology & Laboratory Medicine, Volume 139 (2015) no. 4, pp. 481-493 | DOI

[6] Bačnik, K.; Kutnjak, D.; Pecman, A.; Mehle, N.; Tušek Žnidarič, M.; Gutiérrez Aguirre, I.; Ravnikar, M. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment, Water Research, Volume 177 (2020) | DOI

[7] Baizan-Edge, A.; Cock, P.; MacFarlane, S.; McGavin, W.; Torrance, L.; Jones, S. Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data, Journal of General Virology, Volume 100 (2019) no. 3, pp. 533-542 | DOI

[8] Bakker, M. G. A fungal mock community control for amplicon sequencing experiments, Molecular Ecology Resources, Volume 18 (2018) no. 3, pp. 541-556 | DOI

[9] Bérubé, J. A.; Gagné, P. N.; Ponchart, J. P.; Tremblay, É. D.; Bilodeau, G. J. Detection of Diplodia corticola spores in Ontario and Québec based on High Throughput Sequencing (HTS) methods, Canadian Journal of Plant Pathology, Volume 40 (2018) no. 3, pp. 378-386 | DOI

[10] Bester, R.; Cook, G.; Breytenbach, J. H. J.; Steyn, C.; De Bruyn, R.; Maree, H. J. Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids, Virology Journal, Volume 18 (2021) no. 1 | DOI

[11] Bonants, P.; Griekspoor, Y.; Houwers, I.; Krijger, M.; van der Zouwen, P.; van der Lee, T. A. J.; van der Wolf, J. Development and Evaluation of a Triplex TaqMan Assay and Next-Generation Sequence Analysis for Improved Detection of Xylella in Plant Material, Plant Disease, Volume 103 (2019) no. 4, pp. 645-655 | DOI

[12] Boukari, W.; Mollov, D.; Wei, C.; Tang, L.; Grinstead, S.; Tahir, M. N.; Mulandesa, E.; Hincapie, M.; Beiriger, R.; Rott, P. Screening for sugarcane yellow leaf virus in sorghum in Florida revealed its occurrence in mixed infections with sugarcane mosaic virus and a new marafivirus, Crop Protection, Volume 139 (2021) | DOI

[13] Brinkmann, A.; Andrusch, A.; Belka, A.; Wylezich, C.; Höper, D.; Pohlmann, A.; Nordahl Petersen, T.; Lucas, P.; Blanchard, Y.; Papa, A.; Melidou, A.; Oude Munnink, B. B.; Matthijnssens, J.; Deboutte, W.; Ellis, R. J.; Hansmann, F.; Baumgärtner, W.; van der Vries, E.; Osterhaus, A.; Camma, C.; Mangone, I.; Lorusso, A.; Marcacci, M.; Nunes, A.; Pinto, M.; Borges, V.; Kroneman, A.; Schmitz, D.; Corman, V. M.; Drosten, C.; Jones, T. C.; Hendriksen, R. S.; Aarestrup, F. M.; Koopmans, M.; Beer, M.; Nitsche, A. Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets, Journal of Clinical Microbiology, Volume 57 (2019) no. 8 | DOI

[14] Bruni, I.; Galimberti, A.; Caridi, L.; Scaccabarozzi, D.; De Mattia, F.; Casiraghi, M.; Labra, M. A DNA barcoding approach to identify plant species in multiflower honey, Food Chemistry, Volume 170 (2015), pp. 308-315 | DOI

[15] Budowle, B.; Connell, N. D.; Bielecka-Oder, A.; Colwell, R. R.; Corbett, C. R.; Fletcher, J.; Forsman, M.; Kadavy, D. R.; Markotic, A.; Morse, S. A.; Murch, R. S.; Sajantila, A.; Schmedes, S. E.; Ternus, K. L.; Turner, S. D.; Minot, S. Validation of high throughput sequencing and microbial forensics applications, Investigative Genetics, Volume 5 (2014) no. 1 | DOI

[16] Caruso, P.; Palomo, J. L.; Bertolini, E.; Álvarez, B.; López, M. M.; Biosca, E. G. Seasonal Variation of Ralstonia solanacearum Biovar 2 Populations in a Spanish River: Recovery of Stressed Cells at Low Temperatures, Applied and Environmental Microbiology, Volume 71 (2005) no. 1, pp. 140-148 | DOI

[17] Chandelier, A.; Hulin, J.; San Martin, G.; Debode, F.; Massart, S. Comparison of qPCR and Metabarcoding Methods as Tools for the Detection of Airborne Inoculum of Forest Fungal Pathogens, Phytopathology, Volume 111 (2021) no. 3, pp. 570-581 | DOI

[18] Christenhusz, G. M.; Devriendt, K.; Dierickx, K. To tell or not to tell? A systematic review of ethical reflections on incidental findings arising in genetics contexts, European Journal of Human Genetics, Volume 21 (2013) no. 3, pp. 248-255 | DOI

[19] Claverie, S.; Bernardo, P.; Kraberger, S.; Hartnady, P.; Lefeuvre, P.; Lett, J.-M.; Galzi, S.; Filloux, D.; Harkins, G. W.; Varsani, A.; Martin, D. P.; Roumagnac, P. From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study, Environmental Virology and Virus Ecology, Elsevier, 2018, pp. 55-83 | DOI

[20] Constantin, E. C.; Haegeman, A.; Van Vaerenbergh, J.; Baeyen, S.; Van Malderghem, C.; Maes, M.; Cottyn, B. Pathogenicity and virulence gene content of Xanthomonas strains infecting Araceae, formerly known as Xanthomonas axonopodis pv. dieffenbachiae, Plant Pathology, Volume 66 (2017) no. 9, pp. 1539-1554 | DOI

[21] Culbreath, K.; Melanson, S.; Gale, J.; Baker, J.; Li, F.; Saebo, O.; Kommedal, O.; Contreras, D.; Garner, O. B.; Yang, S. Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids, The Journal of Molecular Diagnostics, Volume 21 (2019) no. 5, pp. 913-923 | DOI

[22] Cummings, L. A.; Kurosawa, K.; Hoogestraat, D. R.; SenGupta, D. J.; Candra, F.; Doyle, M.; Thielges, S.; Land, T. A.; Rosenthal, C. A.; Hoffman, N. G.; Salipante, S. J.; Cookson, B. T. Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples, Clinical Chemistry, Volume 62 (2016) no. 11, pp. 1465-1473 | DOI

[23] Denman, S.; Doonan, J.; Ransom-Jones, E.; Broberg, M.; Plummer, S.; Kirk, S.; Scarlett, K.; Griffiths, A. R.; Kaczmarek, M.; Forster, J.; Peace, A.; Golyshin, P. N.; Hassard, F.; Brown, N.; Kenny, J. G.; McDonald, J. E. Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline, The ISME Journal, Volume 12 (2018) no. 2, pp. 386-399 | DOI

[24] Di Gaspero, G.; Radovic, S.; De Luca, E.; Spadotto, A.; Magris, G.; Falginella, L.; Cattonaro, F.; Marroni, F. Evaluation of sensitivity and specificity in RNA-Seq-based detection of grapevine viral pathogens, Journal of Virological Methods, Volume 300 (2022) | DOI

[25] Elbrecht, V.; Braukmann, T. W.; Ivanova, N. V.; Prosser, S. W.; Hajibabaei, M.; Wright, M.; Zakharov, E. V.; Hebert, P. D.; Steinke, D. Validation of COI metabarcoding primers for terrestrial arthropods, PeerJ, Volume 7 (2019) | DOI

[26] Fox, A. Reconsidering causal association in plant virology, Plant Pathology, Volume 69 (2020) no. 6, pp. 956-961 | DOI

[27] Fox, A.; Fowkes, A. R.; Skelton, A.; Harju, V.; Buxton‐Kirk, A.; Kelly, M.; Forde, S. M. D.; Pufal, H.; Conyers, C.; Ward, R.; Weekes, R.; Boonham, N.; Adams, I. P. Using high‐throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae), Plant Pathology (2019) | DOI

[28] Fuentes, S.; Jones, R. A. C.; Matsuoka, H.; Ohshima, K.; Kreuze, J.; Gibbs, A. J. Potato virus Y; the Andean connection, Virus Evolution, Volume 5 (2019) no. 2 | DOI

[29] Gaafar, Y.; Lüddecke, P.; Heidler, C.; Hartrick, J.; Sieg‐Müller, A.; Hübert, C.; Wichura, A.; Ziebell, H. First report of Southern tomato virus in German tomatoes, New Disease Reports, Volume 40 (2019) no. 1, p. 1-1 | DOI

[30] Gaafar, Y. Z. A.; Ziebell, H. Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing, PLOS ONE, Volume 15 (2020) no. 8 | DOI

[31] Galan, M.; Razzauti, M.; Bard, E.; Bernard, M.; Brouat, C.; Charbonnel, N.; Dehne-Garcia, A.; Loiseau, A.; Tatard, C.; Tamisier, L.; Vayssier-Taussat, M.; Vignes, H.; Cosson, J.-F. 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife, mSystems, Volume 1 (2016) no. 4 | DOI

[32] Hagen, C.; Frizzi, A.; Gabriels, S.; Huang, M.; Salati, R.; Gabor, B.; Huang, S. Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification, Archives of Virology, Volume 157 (2012) no. 5, pp. 907-915 | DOI

[33] Hanafi, M.; Rong, W.; Tamisier, L.; Berhal, C.; Roux, N.; Massart, S. Detection of Banana Mild Mosaic Virus in Musa In Vitro Plants: High-Throughput Sequencing Presents Higher Diagnostic Sensitivity Than (IC)-RT-PCR and Identifies a New Betaflexiviridae Species, Plants, Volume 11 (2022) no. 2 | DOI

[34] Hanssen, I. M.; Paeleman, A.; Vandewoestijne, E.; Van Bergen, L.; Bragard, C.; Lievens, B.; Vanachter, A. C. R. C.; Thomma, B. P. H. J. Pepino mosaic virus isolates and differential symptomatology in tomato, Plant Pathology, Volume 58 (2009) no. 3, pp. 450-460 | DOI

[35] Hardwick, S. A.; Chen, W. Y.; Wong, T.; Kanakamedala, B. S.; Deveson, I. W.; Ongley, S. E.; Santini, N. S.; Marcellin, E.; Smith, M. A.; Nielsen, L. K.; Lovelock, C. E.; Neilan, B. A.; Mercer, T. R. Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis, Nature Communications, Volume 9 (2018) no. 1 | DOI

[36] Hébrant, A.; Froyen, G.; Maes, B.; Salgado, R.; Le Mercier, M.; D’haene, N.; De Keersmaecker, S.; Claes, K.; Van Der Meulen, J.; Aftimos, P.; Van Houdt, J.; Cuppens, K.; Vanneste, K.; Dequeker, E.; Van Dooren, S.; Van Huysse, J.; Nollet, F.; Van Laere, S.; Denys, B.; Ghislain, V.; Van Campenhout, C.; Van Den Bulcke, M. The Belgian next generation sequencing guidelines for haematological and solid tumours, The Belgian Journal of Medical Oncology, Volume 11 (2017)

[37] Herren, G. L.; Habraken, J.; Waeyenberge, L.; Haegeman, A.; Viaene, N.; Cougnon, M.; Reheul, D.; Steel, H.; Bert, W. Effects of synthetic fertilizer and farm compost on soil nematode community in long-term crop rotation plots: A morphological and metabarcoding approach, PLOS ONE, Volume 15 (2020) no. 3 | DOI

[38] Hou, W.; Li, S.; Massart, S. Is There a “Biological Desert” With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses, Frontiers in Microbiology, Volume 11 (2020) | DOI

[39] Jennings, L. J.; Arcila, M. E.; Corless, C.; Kamel-Reid, S.; Lubin, I. M.; Pfeifer, J.; Temple-Smolkin, R. L.; Voelkerding, K. V.; Nikiforova, M. N. Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels, The Journal of Molecular Diagnostics, Volume 19 (2017) no. 3, pp. 341-365 | DOI

[40] Kesanakurti, P.; Belton, M.; Saeed, H.; Rast, H.; Boyes, I.; Rott, M. Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control, Journal of Virological Methods, Volume 236 (2016), pp. 35-40 | DOI

[41] Kopylova, E.; Noé, L.; Touzet, H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics, Volume 28 (2012) no. 24, pp. 3211-3217 | DOI

[42] Lamichhane, J. R.; Venturi, V. Synergisms between microbial pathogens in plant disease complexes: a growing trend, Frontiers in Plant Science, Volume 06 (2015) | DOI

[43] Lebas, B.; Adams, I.; Al Rwahnih, M.; 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. J.; Sultmanis, S.; van der Vlugt, R.; 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, EPPO Bulletin, Volume 52 (2022) no. 2, pp. 394-418 | DOI

[44] Locati, M. D.; Terpstra, I.; de Leeuw, W. C.; Kuzak, M.; Rauwerda, H.; Ensink, W. A.; van Leeuwen, S.; Nehrdich, U.; Spaink, H. P.; Jonker, M. J.; Breit, T. M.; Dekker, R. J. Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization, Nucleic Acids Research, Volume 43 (2015) no. 14 | DOI

[45] Maclot, F.; Candresse, T.; Filloux, D.; Malmstrom, C. M.; Roumagnac, P.; van der Vlugt, R.; Massart, S. Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales, Frontiers in Microbiology, Volume 11 (2020) | DOI

[46] Malapi-Wight, M.; Salgado-Salazar, C.; Demers, J. E.; Clement, D. L.; Rane, K. K.; Crouch, J. A. Sarcococca Blight: Use of Whole-Genome Sequencing for Fungal Plant Disease Diagnosis, Plant Disease, Volume 100 (2016) no. 6, pp. 1093-1100 | DOI

[47] Maree, H. J.; Fox, A.; Al Rwahnih, M.; Boonham, N.; Candresse, T. Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges, Frontiers in Plant Science, Volume 9 (2018) | DOI

[48] Martin, R. R.; James, D.; Lévesque, C. A. Impacts of Molecular Diagnostic Technologies on Plant Disease Management, Annual Review of Phytopathology, Volume 38 (2000) no. 1, pp. 207-239 | DOI

[49] Marzano, S.-Y. L.; Domier, L. L. Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes, Virus Research, Volume 213 (2016), pp. 332-342 | DOI

[50] Massart, S.; Candresse, T.; Gil, J.; Lacomme, C.; Predajna, L.; Ravnikar, M.; Reynard, J.-S.; Rumbou, A.; Saldarelli, P.; Škorić, D.; Vainio, E. J.; Valkonen, J. P. T.; Vanderschuren, H.; Varveri, C.; Wetzel, T. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies, Frontiers in Microbiology, Volume 8 (2017) | DOI

[51] Massart, S.; Chiumenti, M.; De Jonghe, K.; Glover, R.; Haegeman, A.; Koloniuk, I.; Komínek, P.; Kreuze, J.; Kutnjak, D.; Lotos, L.; Maclot, F.; Maliogka, V.; Maree, H. J.; Olivier, T.; Olmos, A.; Pooggin, M. M.; Reynard, J.-S.; Ruiz-García, A. B.; Safarova, D.; Schneeberger, P. H. H.; Sela, N.; Turco, S.; Vainio, E. J.; Varallyay, E.; Verdin, E.; Westenberg, M.; Brostaux, Y.; Candresse, T. Virus Detection by High-Throughput Sequencing of Small RNAs: Large-Scale Performance Testing of Sequence Analysis Strategies, Phytopathology, Volume 109 (2019) no. 3, pp. 488-497 | DOI

[52] Massart, S.; Olmos, A.; Jijakli, H.; Candresse, T. Current impact and future directions of high throughput sequencing in plant virus diagnostics, Virus Research, Volume 188 (2014), pp. 90-96 | DOI

[53] Mehle, N.; Dreo, T.; Jeffries, C.; Ravnikar, M. Descriptive assessment of uncertainties of qualitative real-time PCR for detection of plant pathogens and quality performance monitoring, EPPO Bulletin, Volume 44 (2014) no. 3, pp. 502-509 | DOI

[54] Miller, S.; Naccache, S. N.; Samayoa, E.; Messacar, K.; Arevalo, S.; Federman, S.; Stryke, D.; Pham, E.; Fung, B.; Bolosky, W. J.; Ingebrigtsen, D.; Lorizio, W.; Paff, S. M.; Leake, J. A.; Pesano, R.; DeBiasi, R.; Dominguez, S.; Chiu, C. Y. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid, Genome Research, Volume 29 (2019) no. 5, pp. 831-842 | DOI

[55] Mirghasempour, S. A.; Huang, S.; Studholme, D. J.; Brady, C. L. A Grain Rot of Rice in Iran Caused by a Xanthomonas Strain Closely Related to X. sacchari, Plant Disease, Volume 104 (2020) no. 6, pp. 1581-1583 | DOI

[56] Murugan, S.; Kumarasinghe, L. An operational risk assessment framework for a plant health diagnostic laboratory, EPPO Bulletin, Volume 48 (2018) no. 2, pp. 225-233 | DOI

[57] Núñez, A.; Amo de Paz, G.; Ferencova, Z.; Rastrojo, A.; Guantes, R.; García, A. M.; Alcamí, A.; Gutiérrez-Bustillo, A. M.; Moreno, D. A. Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing, Applied and Environmental Microbiology, Volume 83 (2017) no. 13 | DOI

[58] Olmos, A.; Boonham, N.; Candresse, T.; Gentit, P.; Giovani, B.; Kutnjak, D.; Liefting, L.; Maree, H.; Minafra, A.; Moreira, A.; Nakhla, M.; Petter, F.; Ravnikar, M.; Rodoni, B.; Roenhorst, J.; Rott, M.; Ruiz-García, A.; Santala, J.; Stancanelli, G.; van der Vlugt, R.; Varveri, C.; Westenberg, M.; Wetzel, T.; Ziebell, H.; Massart, S. High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities, EPPO Bulletin, Volume 48 (2018) no. 2, pp. 219-224 | DOI

[59] Orlando, V.; Grove, I. G.; Edwards, S. G.; Prior, T.; Roberts, D.; Neilson, R.; Back, M. Root‐lesion nematodes of potato: Current status of diagnostics, pathogenicity and management, Plant Pathology, Volume 69 (2020) no. 3, pp. 405-417 | DOI

[60] Castagnone-Sereno, P.; Skantar, A.; Robertson, L. Molecular Tools for Diagnostics, Genomics and Molecular Genetics of Plant-Nematode Interactions, Springer Netherlands, Dordrecht, 2011, pp. 443-464 | DOI

[61] Palmer, J. M.; Jusino, M. A.; Banik, M. T.; Lindner, D. L. Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data, PeerJ, Volume 6 (2018) | DOI

[62] Pecman, A.; Kutnjak, D.; Gutiérrez-Aguirre, I.; Adams, I.; Fox, A.; Boonham, N.; Ravnikar, M. Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches, Frontiers in Microbiology, Volume 8 (2017) | DOI

[63] Piper, A. M.; Batovska, J.; Cogan, N. O. I.; Weiss, J.; Cunningham, J. P.; Rodoni, B. C.; Blacket, M. J. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance, GigaScience, Volume 8 (2019) no. 8 | DOI

[64] PM 7/77 (3) Documentation and reporting on a diagnosis, EPPO Bulletin, Volume 49 (2019) no. 3, pp. 527-529 | DOI

[65] PM 7/76 (5) Use of EPPO Diagnostic Standards, EPPO Bulletin, Volume 48 (2018) no. 3, pp. 373-377 | DOI

[66] PM 7/98 (4) Specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity, EPPO Bulletin, Volume 49 (2019) no. 3, pp. 530-563 | DOI

[67] PM 7/147 (1) Guidelines for the production of biological reference material, EPPO Bulletin, Volume 51 (2021) no. 3, pp. 499-506 | DOI

[68] Rehm, H. L.; Bale, S. J.; Bayrak-Toydemir, P.; Berg, J. S.; Brown, K. K.; Deignan, J. L.; Friez, M. J.; Funke, B. H.; Hegde, M. R.; Lyon, E. ACMG clinical laboratory standards for next-generation sequencing, Genetics in Medicine, Volume 15 (2013) no. 9, pp. 733-747 | DOI

[69] Riddell, C. E.; Frederickson-Matika, D.; Armstrong, A. C.; Elliot, M.; Forster, J.; Hedley, P. E.; Morris, J.; Thorpe, P.; Cooke, D. E.; Pritchard, L.; Sharp, P. M.; Green, S. Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain, PeerJ, Volume 7 (2019) | DOI

[70] Roenhorst, J. W.; de Krom, C.; Fox, A.; Mehle, N.; Ravnikar, M.; Werkman, A. W. Ensuring validation in diagnostic testing is fit for purpose: a view from the plant virology laboratory, EPPO Bulletin, Volume 48 (2018) no. 1, pp. 105-115 | DOI

[71] Rolland, M.; Villemot, J.; Marais, A.; Theil, S.; Faure, C.; Cadot, V.; Valade, R.; Vitry, C.; Rabenstein, F.; Candresse, T. Classical and next generation sequencing approaches unravel Bymovirus diversity in barley crops in France, PLOS ONE, Volume 12 (2017) no. 11 | DOI

[72] Rong, W.; Rollin, J.; Hanafi, M.; Roux, N.; Massart, S. Validation of high throughput sequencing as virus indexing test for Musa germplasm: performance criteria evaluation and contamination monitoring using an alien control, PhytoFrontiers (2022) | DOI

[73] Roossinck, M. J. Plants, viruses and the environment: Ecology and mutualism, Virology, Volume 479-480 (2015), pp. 271-277 | DOI

[74] Roy, S.; Coldren, C.; Karunamurthy, A.; Kip, N. S.; Klee, E. W.; Lincoln, S. E.; Leon, A.; Pullambhatla, M.; Temple-Smolkin, R. L.; Voelkerding, K. V.; Wang, C.; Carter, A. B. Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines, The Journal of Molecular Diagnostics, Volume 20 (2018) no. 1, pp. 4-27 | DOI

[75] Santala, J.; Valkonen, J. P. T. Sensitivity of Small RNA-Based Detection of Plant Viruses, Frontiers in Microbiology, Volume 9 (2018) | DOI

[76] Schlaberg, R.; Chiu, C. Y.; Miller, S.; Procop, G. W.; Weinstock, G. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection, Archives of Pathology & Laboratory Medicine, Volume 141 (2017) no. 6, pp. 776-786 | DOI

[77] Soltani, N.; Stevens, K. A.; Klaassen, V.; Hwang, M.-S.; Golino, D. A.; Al Rwahnih, M. Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics, Viruses, Volume 13 (2021) no. 6 | DOI

[78] Tamisier, L.; Haegeman, A.; Foucart, Y.; Fouillien, N.; Al Rwahnih, M.; Buzkan, N.; Candresse, T.; Chiumenti, M.; De Jonghe, K.; Lefebvre, M.; Margaria, P.; Reynard, J. S.; Stevens, K.; Kutnjak, D.; Massart, S. Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection, Peer Community Journal, Volume 1 (2021) | DOI

[79] Temple, C.; Blouin, A. G.; De Jonghe, K.; Foucart, Y.; Botermans, M.; Westenberg, M.; Schoen, R.; Gentit, P.; Visage, M.; Verdin, E.; Wipf-Scheibel, C.; Ziebell, H.; Gaafar, Y. Z. A.; Zia, A.; Yan, X.-H.; Richert-Pöggeler, K. R.; Ulrich, R.; Rivarez, M. P. S.; Kutnjak, D.; Vučurović, A.; Massart, S. Biological and Genetic Characterization of Physostegia Chlorotic Mottle Virus in Europe Based on Host Range, Location, and Time, Plant Disease (2022) | DOI

[80] Thomsen, P. F.; Sigsgaard, E. E. Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods, Ecology and Evolution, Volume 9 (2019) no. 4, pp. 1665-1679 | DOI

[81] Tourlousse, D. M.; Ohashi, A.; Sekiguchi, Y. Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls, Scientific Reports, Volume 8 (2018) no. 1 | DOI

[82] Tremblay, É. D.; Duceppe, M.-O.; Bérubé, J. A.; Kimoto, T.; Lemieux, C.; Bilodeau, G. J. Screening for Exotic Forest Pathogens to Increase Survey Capacity Using Metagenomics, Phytopathology, Volume 108 (2018) no. 12, pp. 1509-1521 | DOI

[83] Trontin, C.; Agstner, B.; Altenbach, D.; Anthoine, G.; Bagińska, H.; Brittain, I.; Chabirand, A.; Chappé, A. M.; Dahlin, P.; Dreo, T.; Freye‐Minks, C.; Gianinazzi, C.; Harrison, C.; Jones, G.; Luigi, M.; Massart, S.; Mehle, N.; Mezzalama, M.; Mouaziz, H.; Petter, F.; Ravnikar, M.; Raaymakers, T. M.; Renvoisé, J. P.; Rolland, M.; Santos Paiva, M.; Seddas, S.; Vlugt, R.; Vučurović, A. VALITEST: Validation of diagnostic tests to support plant health, EPPO Bulletin, Volume 51 (2021) no. 1, pp. 198-206 | DOI

[84] van Boheemen, S.; van Rijn, A. L.; Pappas, N.; Carbo, E. C.; Vorderman, R. H.; Sidorov, I.; van `t Hof, P. J.; Mei, H.; Claas, E. C.; Kroes, A. C.; de Vries, J. J. Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients, The Journal of Molecular Diagnostics, Volume 22 (2020) no. 2, pp. 196-207 | DOI

[85] Visser, M.; Bester, R.; Burger, J. T.; Maree, H. J. Next-generation sequencing for virus detection: covering all the bases, Virology Journal, Volume 13 (2016) no. 1 | DOI

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