Agronomy and Crop Science; Plant Science; Horticulture
Abstract :
[en] 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.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Lebas, Benedicte; Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
Adams, Ian; FERA Science Ltd, York Biotechnology Campus, York, United Kingdom
Al Rwahnih, Maher; Department of Plant Pathology, University of California-Davis, Davis, United States
Baeyen, Steve; Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
Bilodeau, Guillaume J.; Canadian Food Inspection Agency, Ottawa, Canada
Blouin, Arnaud G.; Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
Boonham, Neil; Institute for Agrifood Research Innovations, Newcastle University, Newcastle upon Tyne, United Kingdom
Candresse, Thierry; UMR Biologie du Fruit et Pathologie, Université de Bordeaux, INRAE, Villenave d'Ornon, France
Chandelier, Anne; Walloon Agricultural Research Centre, CraW, Gembloux, Belgium
De Jonghe, Kris; Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
Fox, Adrian; FERA Science Ltd, York Biotechnology Campus, York, United Kingdom
Gaafar, Yahya Z. A.; Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
Gentit, Pascal; Unité de Bactériologie, Plant Health Laboratory, Virologie et détection des OGM, ANSES, Angers, France
Haegeman, Annelies; Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
Ho, Wellcome; Plant Health Diagnostic Laboratory, Ministry for Primary Industries, Auckland, New Zealand
Hurtado-Gonzales, Oscar; Plant Germplasm and Quarantine Program, USDA-APHIS, PPQ, Beltsville, United States
Kreuze, Jan; CGIAR, Consultative Group for International Agricultural Research, Lima, Peru
Kutjnak, Denis; Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
Landa, Blanca; Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
Liu, Mingxin; School of Natural Sciences, University of Tasmania, Burnie, Australia
Maclot, François ; Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
Malapi-Wight, Martha; Biotechnology Risk Analysis Programs, USDA-APHIS, BRS, Washington, United States
Maree, Hano J.; Department of Genetics, Stellenbosch University, Matieland, South Africa ; Citrus Research International, Matieland, South Africa
Martoni, Francesco; Agriculture Victoria, AgriBio Centre for AgriBiosciences, Bundoora, Australia
Mehle, Natasha; Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
Minafra, Angelantonio; IPSP-CNR, Institute for Sustainable Plant Protection, Consiglio Nazionale delle Ricerche, Bari, Italy
Mollov, Dimitre; Horticultural Crops Research Unit, USDA-ARS, Corvallis, United States
Moreira, Adriana; FAO, International Plant Protection Convention, Rome, Italy
Nakhla, Mark; Science and Technology, USDA-APHIS, PPQ, Hanover, United States
Petter, Françoise; European and Mediterranean Plant Protection Organization, Paris, France
Piper, Alexander M.; Agriculture Victoria, AgriBio Centre for AgriBiosciences, Bundoora, Australia
Ponchart, Julien; Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
Rae, Robbie; School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
Remenant, Benoit; Unité de Bactériologie, Plant Health Laboratory, Virologie et détection des OGM, ANSES, Angers, France
Rivera, Yazmin; Science and Technology, USDA-APHIS, PPQ, Hanover, United States
Rodoni, Brendan; Agriculture Victoria, AgriBio Centre for AgriBiosciences, Bundoora, Australia
Roenhorst, Johanna W.; Netherlands Food and Consumer Product Safety Authority, National Plant Protection Organization, Wageningen, Netherlands
Rollin, Johan ; Université de Liège - ULiège > TERRA Research Centre
Saldarelli, Pasquale; IPSP-CNR, Institute for Sustainable Plant Protection, Consiglio Nazionale delle Ricerche, Bari, Italy
Santala, Johanna; Plant Analytics, Finnish Food Authority, Helsinki, Finland
Souza-Richards, Rose; International Seed Federation, Nyon, Switzerland
Spadaro, Davide; Department of Agricultural, Forest and Food Sciences and AGROINNOVA – Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
Studholme, David J.; Biosciences, University of Exeter, Exeter, United Kingdom
Sultmanis, Stefanie; Canadian Food Inspection Agency, Ottawa, Canada
van der Vlugt, René; Wageningen University and Research, Wageningen, Netherlands
Tamisier, Lucie; Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
Trontin, Charlotte; European and Mediterranean Plant Protection Organization, Paris, France
Vazquez-Iglesias, Ines; FERA Science Ltd, York Biotechnology Campus, York, United Kingdom
Vicente, Claudia S. L.; Instituto Nacional de Investigação Agrária e Veterinária (INIAV I.P.), Quinta do Marquês, Oeiras, Portugal
Vossenberg, Bart T. L. H.; Netherlands Food and Consumer Product Safety Authority, National Plant Protection Organization, Wageningen, Netherlands
Wetzel, Thierry; DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
Ziebell, Heiko; Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
Massart, Sébastien ; Université de Liège - ULiège > TERRA Research Centre > Gestion durable des bio-agresseurs
This article is based upon work from the work package 2 of the project VALITEST ( https://www.valitest.eu/ ), supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 773139.
Abdelfattah A, Sanzani SM, Wisniewski M, Berg G, Cacciola SO, Schena L (2019) Revealing cues for fungal interplay in the plant-air interface in vineyards. Frontiers in Plant Science 10, 922.
Adams IP, Fox A (2016) Diagnosis of plant viruses using next-generation sequencing and metagenomics analysis. In: Wang A, Zhou X (eds.), Current research topics in plant virology, Springer International Publishing, Switzerland, pp. 323–335.
Adams IP, Fox A, Boonham N, Massart S, De Jonghe K (2018) The impact of high throughput sequencing on plant health diagnostics. European Journal of Plant Pathology 152, 909–919.
Aguayo J, Fourrier-Jeandel C, Husson C, Ioos R (2018) Assessment of passive traps combined with high-throughput sequencing to study airborne fungal communities. Applied and Environmental Microbiology 84, e02637-17.
Ahmed M, Back MA, Prior T, Karssen G, Lawson R, Adams I, Sapp M (2019) Metabarcoding of soil nematodes: the importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s). Metabarcoding and Metagenomics 3, 77–99.
Al Rwahnih M, Daubert S, Golino D, Islas C, Rowhani A (2015) Comparison of next-generation sequencing versus biological indexing for the optimal detection of viral pathogens in grapevine. Phytopathology 105, 758–763.
An J-H, Noh Y-H, Kim Y-E, Lee H-I, Cha J-S (2015) Development of PCR and TaqMan PCR assays to detect Pseudomonas coronafaciens, a causal agent of Halo blight of oats. The Plant Pathology Journal 31(1), 25–32.
Anslan S., Nilsson R.H., Wurzbacher C., Baldrian P., Tedersoo L., Bahram M. (2018) Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys, 39: 29. https://doi.org/10.3897/mycokeys.39.28109.
Aritua V, Musoni A, Kabeja A, Butare L, Mukamuhirwa F, Gahakwa D, Kato F, Abang MM, Buruchara R, Sapp M, Harrison J, Studholme DJ, Smith J (2015) The draft genome sequence of Xanthomonas species strain Nyagatare, isolated from diseased bean in Rwanda. FEMS Microbiology Letters 362(4), 1–4.
Asplund M, Kjartansdóttir KR, Mollerup S, Vinner L, Fridholm H, Herrera JAR, Friis-Nielsen J, Hansen TA, Jensen RH, Nielsen IB, Richter SR, Rey-Iglesia A, Matey-Hernandez ML, Alquezar-Planas DE, Olsen PVS, Sicheritz-Pontén T, Willerslev E, Lund O, Brunak S, Mourier T, Nielsen LP, Izarzugaza JMG, Hansen AJ (2019) Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries. Clinical Microbiology and Infection 25(10), 1277–1285.
Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, Gibson JS, Grody WW, Hegde MR, Hoeltge GA, Leonard DGB, Merker JD, Nagarajan R, Palicji LA, Robetorye RS, Schrijver I, Weck KE, Voelkerding KV (2015) College of American Pathologists' laboratory standards for next-generation sequencing clinical tests. Archives of Pathology & Laboratory Medicine 139, 481–493.
Bačnik K, Kutnjak D, Pecman A, Mehle N, Tušek Žnidarič M, Gutiérrez Aguirre I, Ravnikar M (2020) Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment. Water research 177, 115628.
Baizan-Edge A, Cock P, MacFarlane S, McGavin W, Torrance L, Jones S. (2019) Kodoja: a workflow for virus detection in plants using k-mer analysis of RNA-sequencing data. Journal of General Virology 100(3), 533–542.
Barba M, Czosnek H, Hadidi A (2014) Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6, 106–136.
Batovska J, Piper AM, Valenzuela I, Cunningham JP, Blacket MJ (2021) Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches. Scientific Reports 11, 7946.
Bester R, Cook G, Breytenbach JH, Steyn C, De Bruyn R, Maree HJ (2021) 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 18(1), 1–9.
Bonants PJM, van Gent-Pelzer MPE, van Leeuwen GCM, van der Lee TAJ (2015) A real-time TaqMan PCR assay to discriminate between pathotype 1 (D1) and non-pathotype 1 (D1) isolates of Synchytrium endobioticum. European Journal of Plant Pathology 143, 495–506.
Braukmann TWA, Ivanova NV, Prosser SWJ, Elbrecht V, Steinke D, Ratnasingham S, de Waard JR, Sones JE, Zakhhharov EV, Hebert PDN (2019) Metabarcoding a diverse arthropod mock community. Molecular Ecology Resources 19, 711–727.
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 BB, Matthijnssens J, Deboutte W, Ellis RJ, Hansmann F, Baumgärtner W, van der Vries E, Osterhaus A, Camma C, Mangone I, Lorusso A, Maracci M, Nunes A, Pinto M, Borges V, Kroneman A, Schmitz D, Corman VM, Drosten C, Jones TC, Hendriksen RS, Aarestrup FM, Koopmans M, Beer M, Nitsche A (2019) Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets. Journal of Clinical Microbiology 57(8), e00466-19.
Bruni I, Galimberti A, Caridi L, Scaccabarozzi D, De Mattia F, Casiraghi M, Labra M (2015) A DNA barcoding approach to identify plant species in multiflower honey. Food Chemistry 170, 308–315.
Budowle B, Donnell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, Forsman M, Kadavy DR, Markotic A, Morse SA, Murch RS, Sajantila A, Schmedes SE, Ternus KL, Turner SD, Minot S (2014) Validation of high throughput sequencing and microbial forensics applications. Investigative Genetics, 5, 9.
Buschmann T, Zhang R, Brash DE, Bystrykh LV (2014). Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate. BMC Bioinformatics 15, 264.
Cai W, Nunziata S, Rascoe J, Stulberg MJ (2019). SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus. Scientific reports 9(1), 1–8.
Candresse T, Filloux D, Muhire B, Julian C, Galzi S, Fort G, Bernardo P, Daugrois JH, Fernandez E, Martin DP, Varsani A (2014) Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLoS One 9(7), e102945.
Carew ME, Coleman RA, Hoffmann AA (2018) Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? PeerJ 6, e4980.
Castro CJ, Ng TFF (2017). U50: A new metric for measuring assembly output based on non-overlapping, target-specific contigs. Journal of Computational Biology 24(11), 1071–1080.
Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J (2021). Trends in molecular diagnosis and diversity studies for phytosanitary regulated Xanthomonas. Microorganisms 9(4), 862.
Cella E, Angeletti S, Fogolari M, Bazzardi R, de Gara L, Ciccozzi M (2018) Two different Xylella fastidiosa strains circulating in Italy: phylogenetic and evolutionary analyses. Journal of Plant Interactions 13, 428–432.
Champlot S, Berthelot C, Pruvost M, Bennett EA, Grance T, Geigl E-M (2019) An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS ONE 5(9), e13042.
Chandelier A, Hulin J, San Martin G, Debode F, Massart S (2021) Comparison of qPCR and metabarcoding methods as tools for the detection of airborne inoculum of forest fungal pathogens. Phytopathology 111(3) 570–81.
Davis MPA, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ (2013) Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods 63, 41–49.
Davis JJ, Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR, Will R, Xia F, Stevens R (2016) Antimicrobial resistance prediction in PATRIC and RAST. Scientific Reports 6, 27030.
Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM (2013) An extensive of read trimming effects on Illumina NGS data analysis. PLoS ONE 8(12), e85024.
Denman S, Doonan J, Ransom-Jones E, Broberg M, Plummer S, Kirk S, Scarlett K, Griffiths AR, Kaczmarek M, Forster J, Peace A, Golyshin PN, Hassard F, Brown N, Kenny JG, McDonald JE (2018) Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute oak decline. The ISME Journal 12, 386–399.
Dickins B, Rebolledo-Jaramillo B, Su MS-W, Paul IM, Blankenberg D, Stoler N, Makova KD, Nekrutenko A (2014) Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. Biotechniques 56(3), 134–141.
Dormontt EE, Van Dijk KJ, Bell KL, Biffin E, Breed MF, Byrne M, Caddy-Retalic S, Encinas-Viso F, Nevill PG, Shapcott A, Young JM (2018) Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections—an Australian perspective. Frontiers in Ecology and Evolution 6, 134.
Elbrecht V, Braukmann TWA, Ivanova NV, Prosser SWJ, Hajibabaei M, Wright M, Zakharov EV, Hebert PDN, Steinke D (2019) Validation of COI metabarcoding primers for terrestrial arthropods. PeerJ 7, e7745.
EPPO PM 7/77 (3) (2019) Documentation and reporting on a diagnosis. EPPO Bulletin 49(3), 527–529.
EPPO PM 7/98 (5) (2021) Specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity. EPPO Bulletin 51; 468–498.
EPPO PM7/129 (2) (2021) DNA barcoding as an identification tool for a number of regulated pests. Bulletin OEPP/EPPO Bulletin 51(1), 100–143.
Fox A, Fowkes AR, Skelton A, Harju V, Buxton-Kirk A, Kelly M, Forde SMD, Pufal H, Conyers C, Ward R, Weekes R (2019) Using high-throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae). Plant Pathology 68(3), 576–587.
Franco Ortega S, Ferrocino I, Adams I, Silvestri S, Spadaro D, Gullino ML, Boonham N (2020) Monitoring and surveillance of aerial mycobiota of rice paddy through DNA metabarcoding and qPCR. Journal of Fungi 6(4), 372. https://doi.org/10.3390/jof6040372
Gaafar YZA, Ziebell H (2020) Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing. PLoS ONE 15(8), e0237951.
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 (2016) 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife. Clinical Science and Epidemiology 1(4), e00032-16.
Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni E, Mason CE, Nagarajan R, Voelkerding KV, Worthey DA, Aziz N, Barnes J, Bennett SF, Bisht H, Church FM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FCL, Lunna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong L-JC, Zehnbauer BA, Zook JM, Lubin IM (2015) Good laboratory practice for clinical next-generation sequencing informatics pipelines. National Biotechnologies 33(7), 689–693.
Gasc C, Ribière C, Parisot N, Beugnot R, Defois C, Petit-Biderre C, Boucher D, Peyretaillade E, Peyret P (2015) Capturing prokaryotic dark matter genomes. Research in microbiology 166(10), 814–830.
Giangacomo C, Mohseni M, Kovar L, Wallace JG (2020) Comparing DNA extraction and 16s amplification methods for plant-associated bacterial communities. bioRxiv, doi: https://doi.org/10.1101/2020.07.23.217901.
Hadidi A, Flores R, Candresse T, Barba M (2016) Next-generation sequencing and genome editing in plant virology. Frontiers in Microbiology 7, 1325.
Hamelin RC, Roe AD (2019) Genomic biosurveillance of forest invasive alien enemies: a story written in code. Evolutionary Applications 13(1), 95–115.
Hanshew AS, Mason CJ, Raffa KF, Currie CR (2013) Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities. Journal of Microbiological Methods 95, 149–155.
Haro C, Anguita-Maeso M, Metsis M, Navas-Cortés JA, Landa BB (2021) Evaluation of established methods for DNA extraction and primer pairs targeting 16S rRNA gene for bacterial microbiota profiling of olive xylem sap. Frontiers in plant science 12, 296.
Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270, 313–321.
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 (2018) The Belgian next generation sequencing guidelines for haematological and solid tumours. The Belgian Journal of Medical Oncology 11(2), 56–67.
IPPC Secretariat (2019) Preparing to use high-throughput sequencing (HTS) technologies as a diagnostic tool for phytosanitary purposes. Commission on Phytosanitary Measures Recommendation No. 8. Rome. Published by FAO on behalf of the Secretariat of the International Plant Protection Convention (IPPC). https://www.ippc.int/en/publications/87199/ [last accessed on 10 October 2021].
Johne R, Müller H, Rector A, van Ranst M, Stevens H (2009) Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends in Microbiology 17(5), 205–211.
Katsiani A, Maliogka VI, Katis N, Svanella-Dumas L, Olmos A, Ruiz-García AB, Marais A, Faure C, Theil S, Lotos L, Candresse T (2018) High-throughput sequencing reveals further diversity of Little Cherry Virus 1 with implications for diagnostics. Viruses 10, 385.
Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJA, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, Yokoi T, Larsson MC, Miwa J, Maule AG, Sahashi N, Jones JT, Berriman M (2011) Genomic insights into the origin of parasitism on the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens 7(9), e1002219.
Kircher M, Sawyer S, Meyer M (2011) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research 40(1), e3.
Kwon S, Lee B, Yoon S (2014) CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing. BMC Bioinformatics 15(Suppl. 9), S10.
Kutnjak D, Tamisier L, Adams I, Boonham N, Candresse T, Chiumenti M, De Jonghe K, Kreuze JF, Lefebvre M, Silva G, Malapi-Wight M, Margaria P, Mavrič Pleško I, McGreig S, Miozzi L, Remenant B, Reunard JS, Rollin J, Rott M, Schumpp O, Massart S, Haegeman A (2021) A primer on the analysis of high-throughput sequencing data for detection of plant viruses. Microorganisms 9(4), 841.
Laehnemann D, Borkhardt A, McHardy AC (2016) Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction. Briefings in Bioinformatics 17(1), 154–179.
Lambert C, Braxton C, Charlebois RL, Deyati A, Duncan P, La Neve F, Malicki HD, Ribrioux S, Rozelle DK, Michaels B, Sun W, Yang Z, Khan AS (2018) Considerations for optimisation of high-throughput sequencing bioinformatic pipelines for virus detection. Viruses 10, 528.
Lasken RS, Stockwell TB (2007) Mechanism of chimera formation during the multiple displacement amplification reaction. BMC Biotechnology 7, 19.
Lefebvre M, Theil S, Ma Y, Candresse T (2019) The VirAnnot pipeline: a resource for automated viral diversity estimation and operational taxonomy units (OUT) assignation for virome sequencing data. Phytobiomes Journal, 3(4), 256–259.
Leifert WR, Glatz RV, Siddiqui MS, Collins SR, Taylor PW, Fenech M (2013). Development of a test to detect and quantify irradiation damage in fruit flies. Final Report for Horticulture Australia Ltd., Project VG09160. https://ausveg.com.au/app/data/technical-insights/docs/130056_VG09160.pdf [last accessed on 28 February 2022].
Lu N, Li J, Bi C, Guo J, Tao Y, Luan K, Tu J, Lu Z (2019) Chimera Miner: an improved chimeric read detection pipeline and its application in single cell sequencing. International Journal of Molecular Sciences 20(8), 1953.
MacConaill LE, Burns RT, Nag A, Coleman HA, Slevin MK, Giorda K, Light M, Lai K, Jarosz M, McNeill MS, Ducar MD, Meyerson M, Thorner AR (2018) Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing. BMC Genomics 19, 30.
Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2015) Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ 3, e1420.
Malapi-Wight M, Salgado-Salazar C, Demers J, Clement DL, Rane K, Crouch JA (2016). Sarcococca Blight: use of whole genome sequencing for fungal plant disease diagnosis. Plant Disease 100(6), 1093–1100.
Malapi-Wight M, Adhikari B, Zhou J, Hendrickson L, Maroon-Lango CJ, McFarland C, Foster JA, Hurtado-Gonzales OP (2021) HTS-based diagnostics of sugarcane viruses: seasonal variation and its implications for accurate detection. Viruses 13(8), 1627.
Maliogka VI, Minafra A, Saldarelli P, Ruiz-García AB, Glasa M, Katis N, Olmos A (2018) Recent advances on detection and characterization of fruit tree viruses using high-throughput sequencing technologies. Viruses 10, 436.
Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG (2020) Next generation sequencing and bioinformatic methodologies for infectious disease research and public health: approaches, applications, and considerations for development of laboratory capacity. The Journal of Infectious Diseases 221(S3), S292-307.
Marquina D, Ronquist F, Łukasik P (2021) The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies. PeerJ 9, e10799.
Martoni F, Nogarotto E, Piper AM, Mann R, Valenzuela I, Eow L, Rako L, Rodoni BC, Blacket MJ (2021) Propylene glycol and non-destructive DNA extractions enable preservation and isolation of insect and hosted bacterial DNA. Agriculture 11(1), 77.
Massart S, Olmos A, Jijaki H, Candresse T (2014) Current impact and future directions of high throughput sequencing in plant virus diagnostic. Virus Research 188(8), 90–96.
Massart S, Candresse T, Gil J, Lacomme C, Predajna L, Ravnikar M, Reynard J-S, Rumbou A, Saldarelli P, Škorić D, Vainio EJ, Valkonen JPT, Vanderschuren H, Varveri C, Wetzel T (2017) A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologies. Frontiers in Microbiology 8, 45.
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 HJ, Olivier T, Olmos A, Pooggin MM, Reynard J-S, Ruiz-García AB, Safarova D, Schneeberger PHH, Sela N, Turco S, Vainio EJ, Varallyay E, Verdin E, Westenberg M, Brostaux Y, Candresse T (2019) Virus detection by high-throughput sequencing of small RNAs: large-scale performance testing of sequence analysis strategies. Phytopathology 109, 488–497.
Massart S, Adams I, Al Rwahnih M, Baeyen S, Bilodeau G, Blouin A, Boonham N, Bruinsma M, Candresse T, Chandelier A, De Jonghe K, Fox A, Gaafar Y, Gentit P, Haegemans A, Ho W, Hurtado-Gonzales O, Jonkers W, Kreuze J, Kutjnak D, Landa B, Leite Vicente C, Liu M, Maclot F, Malapi-Wight M, Maree H, Martoni F, Mehle N, Minafra A, Mollov D, Moreira A, Nakhla M, Petter F, Piper A, Ponchart J, Rae R, Remenant B, Rivera Y, Rodoni B, Roenhorst A, Rollin J, Saldarelli P, Santala J, Souza-Richards R, Spadaro D, Studholme D, Sultmanis S, van der Vlugt R, Tamisier L, Trontin C, Van Vaerenbergh J, Wetzel T, Ziebell H, Lebas BSM (2022) Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests. Manuscript in preparation.
Matthijs G, Souche E, Alders M, Corveleyn A, Eck S, Feenstra I, Race V, Sistermans E, Sturm M, Weiss M, Yntema H, Bakker E, Scheffer H, Bauer P (2016) Guidelines for diagnostic next-generation sequencing. European Journal of Human Genetics 24, 2–5.
Mbareche H, Veillette M, Bilodeau G, Duchaine C (2020) Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based sequencing of bioaerosols, PeerJ 8, e8523.
McInerney P, Adams P, Hadi MZ (2014) Error rate comparison during polymerase chain reaction by DNA polymerase. Molecular Biology International 2014, 287430.
Mehle N, Gutiérrez-Aguirre I, Kutnjak D, Ravnikar M (2018) Water-mediated transmission of plant, animal, and human viruses. Advances in Virus Research 101, 85–128.
Moreau C, Wray B, Czekanski-Moir J, Rubin B (2013) DNA preservation: a test of commonly used preservatives for insects. Invertebrate Systematics 27, 81.
Nicolaisen M, West JS, Sapkota R, Canning GGM, Schoen C, Justesen AF (2017) Fungal communities including plant pathogens in near surface air are similar across Northwestern Europe. Frontiers in Microbiology 8, 1729.
Nielsen M, Gilbert MTP, Pape T, Bohmann K (2019). A simplified DNA extraction protocol for unsorted bulk arthropod samples that maintains exoskeletal integrity. Environmental DNA 1(2), 144–154.
Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L (2019) Mycobiome diversity: high-throughput sequencing and identification of fungi. Microbiology 17, 95–109.
Núñez A, Amo de Paz G, Ferencova Z, Rastrojo A, Guantes R, García AM, Alcami A, Montserrat Gutiérrez-Bustillo A, Moreno DA (2017) Validation of the hirst-type spore trap for simultaneous monitoring of prokaryotic and eukaryotic biodiversity in urban air samples by NGS. Applied and Environmental Microbiology, 83(13), e00472-17.
Olmos A, Boonham N, Candresse T, Gentit P, Giovani B, Kutnjak D, Liefting L, Maree HJ, Minafra A, Moreira A, Nakhla MK, Petter F, Ravnikar M, Rodoni B, Roenhorst JW, Rott M, Ruiz-García AB, Santala J, Stancanelli G, van der Vlugt R, Varveri C, Westenberg M, Wetzel T, Ziebell H, Massart S (2018) High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities. Bulletin OEPP / EPPO Bulletin 48(2), 219–24.
O'Sullivan DM, Doyle RM, Temisak S, Redshaw N, Whale AS, Logan G, Huang J, Fischer N, Amos GC, Preston MD, Marchesi JR (2021). An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. Scientific Reports 11(1), 1–14.
Ovaskainen O, Abrego N, Somervuo P, Palorinne I, Hardwick B, Pitkänen J-M, Andrew NR, Niklaus PA, Schmidt NM, Seibold S, Vogt J, Zakharov EV, Hebert PDN, Roslin T, Ivanova NV (2020) Monitoring fungal communities with the global spore sampling project. Frontiers in Ecology and Evolution 7, 511.
Owati A, Agindotan B, Burrows M (2019) Development and application of real-time and conventional SSR-PCR assays for rapid and sensitive detection of Didymella pisi associated with Ascochyta blight of dry pea. Plant Disease 103, 11.
Palmano S, Saccardo F, Martini M, Ermacora P, Scortichini M, Abbà S, Marzachì C, Loi N, Firrao G (2012) Insights into phytoplasma biology through next generation sequencing. Journal of Plant Pathology 94(4), S4.50.
Pantaleo V, Chiumenti M (Eds.) (2018) Viral Metagenomics. Springer New York. https://doi.org/10.1007/978-1-4939-7683-6.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2014) Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research 25, 1043–1055.
Piombo E, Abdelfattah A, Droby S, Wisniewski M, Spadaro D, Schena L (2021) Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens. Microorganisms 9(1), 188.
Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ (2019) Prospects and challenges if implementing DNA metabarcoding for high-throughput insect surveillance. GigaScience 8, giz092.
Prezelj N, Nikolić P, Gruden K, Ravnikar M, Dermastica M (2013) Spatiotemporal distribution of flavescence dorée phytoplasma in grapevine. Plant Pathology 62(4), 760–766.
Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK (2016) Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Analytical Methods 8, 12–24.
Quail MA, Smith M, Jackson D, Leonard S, Skelly T, Swerdlow HP, Gu Y, Ellis P (2014) SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing. BMC Genomics 15, 110.
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC bioinformatics 12(1), 38.
Ratnasingham S, Hebert PDN (2007) BOLD: The Barcode of Life Data System. Molecular Ecology Notes 7, 355–364. https://www.barcodinglife.org.
Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hedge MR, Lyon Y (2013) ACMG clinical laboratory standards for next-generation sequencing. Genetics in Medicine 15(9), 733–747.
Ritari J, Salojärvi J, Lahti, L, de Vos WM (2015) Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database. BMC Genomics 16, 1056.
Ritter CD, Häggqvist S, Karlsson D, Sääksjärvi IE, Muasya AM, Nilsson RH, Antonelli A (2019) Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding. Genome 62(3), 147–159.
Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Kutnjak D (2021) Global advances in tomato virome research: current status and the impact of high-throughput sequencing. Frontiers in Microbiology 12, 671925.
Robinson CV, Porter TM, Wright MTG, Hajibabaei M (2021) Propylene glycol-based antifreeze is an effective preservative for DNA metabarcoding of benthic arthropods. Freshwater Science 40(1), 77–87.
Rosseel T, Pardon B, De Clercq K, Ozhelvaci O, Van Borm S (2014) False-positive results in metagenomics virus discovery: a strong case for follow-up diagnosis. Transboundary and Emerging Diseases 61, 293–299.
Rott M, Xiang Y, Boyes I, Belton M, Saeed H, Kesanakurti P, Hayes S, Lawrence T, Birch C, Bhagwat B, Rast H (2017) Application of next generation sequencing for diagnostic testing of tree fruit viruses and viroids. Plant Disease 101, 1489–1499, https://doi.org/10.1094/PDIS-03-17-0306-RE.
Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter AB (2018) Standards and guidelines for validating next-generation sequencing bioinformatic pipelines, a joint recommendation of the Association for Molecular Pathology and the College of American Pathologists. The Journal of Molecular Diagnostics 20(1), 4–27.
Sahlin K, Chikhi R, Arvestad L (2016) Assembly scaffolding with PE-contaminated mate-pair libraries. Bioinformatics 32(13), 1925–1932.
Scibetta S, Schena L, Abdelfattah A, Pangallo S, Cacciola S (2018) Selection and experimental evaluation of universal primers to study the fungal microbiome of higher plants. Phytobiomes 2(4), 225–236.
Seppey M, Manni M, Zdobnov EM (2019) BUSCO: assessing genome assembly and annotation completeness. In: Kollmar (eds.) Gene Prediction. Methods in Molecular Biology, Humana, New York, vol. 1962, 227–245.
Sharma S, Chatterjee S, Datta S, Prasad R, Dubey D, Prasad RK, Vairale MG (2017) Bacteriophages and its applications: an overview. Folia Microbiology 62, 17–55.
Simpson AJG, Reinach FC, Arruda P, Abreu FA, Acencio M, Alvarenga R, Alves LMC, Araya JE, Baia GS, Baptista CS, Barros MH, Bonaccorsi ED, Bordin S, Bové JM, Briones MRS, Bueno MRP, Camargo AA, Camargo LEA, Carraro DM, Carrer H, Colauto NB, Colombo C, Costa FF, Costa MCR, Costa-Neto CM, Coutinho LL, Cristofani M, Dias-Neto E, Docena C, El-Dorry H, Facincani AP, Ferreira AJS, Ferreira VCA, Ferro JA, Fraga JS, França SC, Franco MC, Frohme M, Furlan LR, Garnier M, Goldman GH, Goldman MHS, Gomes SL, Gruber A, Ho PL, Hoheisel JD, Junqueira ML, Kemper EL, Kitajima JP, Krieger JE, Kuramae EE, Laigret F, Lambais MR, Leite LCC, Lemos EGM, Lemos MVF, Lopes SA, Lopes CR, Machado JA, Machado MA, Madeira AMBN, Madeira HMF, Marino CL, Marques MV, Martins EAL, Martins EMF, Matsukuma AY, Menck CFM, Miracca EC, Miyaki CY, Monteiro-Vitorello CB, Moon DH, Nagai MA, Nascimento ALTO, Netto LES, Nhani Jr A, Nobrega FG, Nunes LR, Oliveira MA, de Oliveira MC, de Oliveira RC, Palmieri DA, Paris A, Peixoto BR, Pereira GAG, Pereira Jr HA, Pesquero JB, Quaggio RB, Roberto PG, Rodrigues V, De M Rosa AJ, De Rosa Jr VE, De Sá RG, Santelli RV, Sawasaki HE, Da Silva ACR, Da Silva AM, Da Silva FR, Silva Jr WA, Da Silveira JF, Silvestri MLZ, Siqueira WJ, De Souza AA, De Souza AP, Terenzi MF, Truffi D, Tsai SM, Tsuhako MH, Vallada H, Van Sluys MA, Verjovski-Almeida S, Vettore AL, Zago MA, Zatz M, Meidanis J, Setubal JC (2000) The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406, 151–159.
Solden L, Lloyd K, Wrighton K (2016) The bright side of microbial dark matter: lessons learned from the uncultivated majority. Current Opinion in Microbiology 31, 217–226.
Soltani N, Stevens KA, Klaassen V, Hwang MS, Golino DA, Al Rwahnih M (2021) Quality assessment and validation of high-throughput sequencing for grapevine virus diagnostics. Viruses 13, 1130.
Sundin GW, Wang N (2018) Antibiotic resistance in plant-pathogenic bacteria. Annual Review of phytopathology 56, 161–80.
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 JS, Stevens K, Kuxtnjak D, Massart, S (2021). Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection. Peer Community Journal 1, https://doi.org/10.24072/pcjournal.62 [last accessed on 28 February 2022].
Taylor GS, Martoni F (2020) Case of mistaken identity: resolving the taxonomy between Trioza eugeniae Froggatt and T. adventicia Tuthill (Psylloidea: Triozidae). Bulletin of Entomological Research 110(3), 340–351.
Tremblay ED, Duceppe M-O, Bérubé JA, Kimoto T, Lemieux C, Bilodeau GJ (2018) Screening for exotic forest pathogens to increase survey capacity using metagenomics. Phytopathology 108(12), 1509–1521.
Tremblay ED, Duceppe M-O, Thurston GB, Gagnon M-C, Côté M-J, Bilodeau GJ (2019) High-resolution biomonitoring of plant pathogens and plant species using metabarcoding of pollen pellet contents collected from a honeybee hive. Environmental DNA 1, 155–175.
van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K (2018) Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies. Molecular Ecology Resources 20(5), 1171–1181.
van Opijnen T, Camilli A (2013) Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nature Review, Microbiology 11(7), 435–442.
Villamor DEV, Keller KE, Martin R, Tzanetakis I E (2021) Comparison of high throughput sequencing to standard protocols for virus detection in berry crops. Plant Disease, https://doi.org/10.1094/PDIS-05-21-0949-RE [last accessed on 13 October 2021].
Vink CJ, Thomas SM, Paquin P, Hayashi CY, Hedin M (2005). The effects of preservatives and temperatures on arachnid DNA. Invertebrate Systematics 19, 99–104.
Waeyenberge L, de Sutter N, Viaene N, Haegeman A (2019). New insights into nematode DNA-metabarcoding as revealed by the characterization of artificial and spiked nematode communities. Diversity 11, 52.
Weiss MM, Van der Zwaag B, Jongbloed JDH, Vogel MJ, Bruggenwirth HT, Lekanne Derez RH, Mook O, Ruivenkamp CAL, van der Stoep N (2013) Sequencing applications in genome diagnostics: A national collaborative study of Dutch genome diagnostic laboratories. Human Mutation 34(10), 1313–1321.
Wesolowska-Andersen A, Iain Bahl M, Kristiansen K, Sicheritz-Pontén T, Gupta R, Rask Licht T (2014) Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomics analysis. Microbiome 2, 19.
Whitehurst LE, Cunard CE, Reed JN, Worthy SJ, Marsico TD, Lucardi RD, Burgess KS (2020) Preliminary application of DNA barcoding toward the detection of viable plant propagules at an initial, international point-of-entry in Georgia, USA. Biological Invasions 22(5), 1585–1606.
Wilcox TM, Zarn KE, Piggott MP, Young MK, McKelvey KS, Schwartz MK (2018) Capture enrichment of aquatic environmental DNA: a first proof of concept. Molecular Ecology Resources 18(6), 1392–1401.
Wright ES, Vetsigian KH (2016). Quality filtering of Illumina index reads mitigates sample cross-talk. BMC Genomics 17, 876.
Xu J, Wang N (2019) Where are we going with genomics in plant pathogenic bacteria? Genomics 111(4), 729–36.
Yang X, Chockalingam SP, Aluru S (2012) A survey of error-correction methods for next-generation sequencing. Briefings in bioinformatics 14(1), 56–66.
Ye SH, Siddle KJ, Park DJ, Sabeti PC (2019) Benchmarking metagenomics tools for taxonomic classification. Cell 178, 779–794.
Zhao L, Zhang H, Kohnen MV, Prasad KV, Gu L, Reddy AS (2019) Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and nanopore-based direct RNA sequencing. Frontiers in Genetics 10, 253.
Zheng Z, Hou Y, Cai Y, Zhang Y, Li Y, Zhou M (2015) Whole-genome sequencing reveals that mutations in myosin-5 confer resistance to the fungicide phenamacril in Fusarium graminearum. Scientific Reports 5, 8248.
