Adams, I. P.; Fera Science Ltd, Sand Hutton, York, YO41 1LZ, United Kingdom
Fox, A.; Fera Science Ltd, Sand Hutton, York, YO41 1LZ, United Kingdom
Boonham, N.; IAFRI, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE1 7RU, United Kingdom
Massart, Sébastien ; Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Gestion durable des bio-agresseurs
De Jonghe, K.; Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 96, Merelbeke, 9820, Belgium
Language :
English
Title :
The impact of high throughput sequencing on plant health diagnostics
Abdelfattah, A., Li Destri Nicosia, M. G., Cacciola, S. O., Droby, S., & Schena, L. (2015). Metabarcoding analysis of fungal diversity in the Phyllosphere and Carposphere of olive (Olea europaea). PLoS One, 10, e0131069
Adams, I. P., Glover, R. H., Monger, W. A., et al. (2009). Next-generation sequencing and metagenomic analysis: A universal diagnostic tool in plant virology. Molecular Plant Pathology, 10, 537–545
Adams, I. P., Glover, R. H., Monger, W. A., et al. (2011). Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant pathology. In F. J. De Bruijn (Ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (pp. 63–71). New York: Wiley
Adams, I. P., Miano, D. W., Kinyua, Z. M., Wangai, A., Kimani, E., Phiri, N., Reeder, R., Harju, V., Glover, R., Hany, U., Souza-Richards, R., Deb Nath, P., Nixon, T., Fox, A., Barnes, A., Smith, J., Skelton, A., Thwaites, R., Mumford, R., & Boonham, N. (2013). Use of next-generation sequencing for the identification and characterization of Maize chlorotic mottle virus and sugarcane mosaic virus causing maize lethal necrosis in Kenya. Plant Pathology, 62, 741–749
Adams IP, Harju VA, Hodges T, Hany U, Skelton A, Rai S, Deka MK, Smith J, Fox A, Uzayisenga B, Ngaboyisonga C, Uwumukiza B, Rutikanga A, Rutherford M, Ricthis B, Phiri N, Boonham N, (2014a). First report of maize lethal necrosis disease in Rwanda. New Disease Reports 29. 22
Adams, I. P., Skelton, A., Macarthur, R., Hodges, T., Hinds, H., Flint, L., Nath, P. D., Boonham, N., & Fox, A. (2014b). Carrot yellow leaf virus is associated with carrot internal necrosis. PLoS One, 9, e109125
Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J. M., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S. O., Kirchberger, N., Garcia, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E. M., Zumbo, P., Walsh, M., O’Mullan, G. D., Tighe, S., Dudley, J. T., Dunaif, A., Ennis, S., O’Halloran, E., Magalhaes, T. R., Boone, B., Jones, A. L., Muth, T. R., Paolantonio, K. S., Alter, E., Schadt, E. E., Garbarino, J., Prill, R. J., Carlton, J. M., Levy, S., & Mason, C. E. (2015a). Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Systems, 1, 72–87
Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J. M., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S. O., Kirchberger, N., Garcia, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E. M., Zumbo, P., Walsh, M., O’Mullan, G. D., Tighe, S., Dudley, J. T., Dunaif, A., Ennis, S., O’Halloran, E., Magalhaes, T. R., Boone, B., Jones, A. L., Muth, T. R., Paolantonio, K. S., Alter, E., Schadt, E. E., Garbarino, J., Prill, R. J., Carlton, J. M., Levy, S., & Mason, C. E. (2015b). Erratum: Geospatial resolution of human and bacterial diversity with City-scale metagenomics. Cell Systems, 1, 97–97.e3
Ahmed, M., Sapp, M., Prior, T., Karssen, G., & Back, M. (2015). Nematode taxonomy: From morphology to metabarcoding. SOIL Discuss., 2015, 1175–1220
Al Rwahnih, M., Daubert, S., Golino, D., & Rowhani, A. (2009). Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology, 387, 395–401
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. Plant Pathology Journal, 31, 25–32
Anderson, P. K., Cunningham, A. A., Patel, N. G., Morales, F. J., Epstein, P. R., & Daszak, P. (2004). Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends in Ecology & Evolution, 19, 535–544
Baker, R. H. A., Anderson, H., Bishop, S., Macleod, A., Parkinson, N., & Tuffen, M. G. (2014). The UK Plant health risk register: A tool for prioritizing actions. EPPO Bulletin, 44, 187–194
Barba, M., Czosnek, H., & Hadidi, A. (2014). Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses, 6, 106–136
Bonants, P. J. M., Gent-Pelzer, M. P. E., Leeuwen, G. C. M., & Lee, T. J. (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
Buée, M., Reich, M., Murat, C., et al. (2009). 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, 184, 449–456
Bühlmann, A., Pothier, J., Tomlinson, J., et al. (2013a). Genomics-informed design of loop-mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. Pruni at the intraspecific level. Plant Pathology, 62, 475–484
Bühlmann, A., Pothier, J. F., Rezzonico, F., Smits, T. H. M., Andreou, M., Boonham, N., Duffy, B., & Frey, J. E. (2013b). Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight. Journal of Microbiological Methods, 92, 332–339
Burns, K. N., Kluepfel, D. A., Strauss, S. L., Bokulich, N. A., Cantu, D., & Steenwerth, K. L. (2015). Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features. Soil Biology and Biochemistry, 91, 232–247
Chen, P., Jeannotte, R., & Weimer, B. C. (2014). Exploring bacterial epigenomics in the next-generation sequencing era: A new approach for an emerging frontier. Trends in Microbiology, 22, 292–300
Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., Quan, P. L., Briese, T., Hornig, M., Geiser, D. M., Martinson, V., vanEngelsdorp, D., Kalkstein, A. L., Drysdale, A., Hui, J., Zhai, J., Cui, L., Hutchison, S. K., Simons, J. F., Egholm, M., Pettis, J. S., & Lipkin, W. I. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder 99. Science, 318, 283–287
Cunniffe, N. J., Cobb, R. C., Meentemeyer, R. K., Rizzo, D. M., & Gilligan, C. A. (2016). Modeling when, where, and how to manage a forest epidemic, motivated by sudden oak death in California. Proceedings of the National Academy of Sciences, 113, 5640–5645
Dahal, G., Hughes, J. D. A., Thottappilly, G., & Lockhart, B. (1998). Effect of temperature on symptom expression and reliability of banana streak badnavirus detection in naturally infected plantain and banana (Musa spp.). Plant Disease, 82, 16–21
De Clerck, C., Crew, K., Mcmichael, L., et al. (2017). Lessons learned from the virus indexing of Musa germplasm: Insights from a multiyear collaboration. Annals of Applied Biology, 171, 15–27
Duan, Y., Zhou, L., Hall, D. G., Li, W., Doddapaneni, H., Lin, H., Liu, L., Vahling, C. M., Gabriel, D. W., Williams, K. P., Dickerman, A., Sun, Y., & Gottwald, T. (2009). Complete genome sequence of Citrus Huanglongbing bacterium, ‘Candidatus Liberibacter asiaticus’ obtained through metagenomics. Molecular Plant-Microbe Interactions, 22, 1011–1020
Evans, A. S. (1976). Causation and disease: The Henle-Koch postulates revisited. The Yale Journal of Biology and Medicine, 49, 175–195
Eyre, D. W., Cule, M. L., Wilson, D. J., Griffiths, D., Vaughan, A., O'Connor, L., Ip, C. L. C., Golubchik, T., Batty, E. M., Finney, J. M., Wyllie, D. H., Didelot, X., Piazza, P., Bowden, R., Dingle, K. E., Harding, R. M., Crook, D. W., Wilcox, M. H., Peto, T. E. A., & Walker, A. S. (2013). Diverse sources of C. Difficile infection identified on whole-genome sequencing. New England Journal of Medicine, 369, 1195–1205
Fox, A., & Mumford, R. (2017). Plant viruses and viroids in the United Kingdom: An analysis of first detections and novel discoveries from 1980 to 2014. Virus Research, 241, 10–18
Fox, A., Adams, I., Hany, U., et al. (2015). The application of next-generation sequencing for screening seeds for viruses and viroids. Seed Science and Technology, 43, 531–535
Fox A, Fowkes A, Buxton-Kirk A, et al., (2016). First report of Potato aucuba mosaic virus in Solanum jasminoides in the United Kingdom. New Disease Reports 34, 32
Frampton, G. M., Fichtenholtz, A., Otto, G. A., Wang, K., Downing, S. R., He, J., Schnall-Levin, M., White, J., Sanford, E. M., An, P., Sun, J., Juhn, F., Brennan, K., Iwanik, K., Maillet, A., Buell, J., White, E., Zhao, M., Balasubramanian, S., Terzic, S., Richards, T., Banning, V., Garcia, L., Mahoney, K., Zwirko, Z., Donahue, A., Beltran, H., Mosquera, J. M., Rubin, M. A., Dogan, S., Hedvat, C. V., Berger, M. F., Pusztai, L., Lechner, M., Boshoff, C., Jarosz, M., Vietz, C., Parker, A., Miller, V. A., Ross, J. S., Curran, J., Cronin, M. T., Stephens, P. J., Lipson, D., & Yelensky, R. (2013). Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nature Biotechnology, 31, 1023–1031
Fredericks, D. N., & Relman, D. A. (1996). Sequence-based identification of microbial pathogens: A reconsideration of Koch's postulates. Clinical Microbiology Reviews, 9, 18–33
Hayden, E. (2014). Technology: The $1,000 genome. Nature, 507, 294–295
Hill, A. (1965). The Envrionment and disease: Association or causation? Proceedings of the Royal Society of Medicine, 58, 295–300
Hubbard, A., Lewis, C. M., Yoshida, K., Ramirez-Gonzalez, R. H., de Vallavieille-Pope, C., Thomas, J., Kamoun, S., Bayles, R., Uauy, C., & Saunders, D. (2015). Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biology, 16, 23
Jagger, I. C., & Chandler, N. (1934). Big vein, a disease of lettuce. Phytopathology, 24, 1253–1256
Jones, D. R., & Baker, R. H. A. (2007). Introductions of non-native plant pathogens into Great Britain, 1970–2004. Plant Pathology, 56, 891–910
Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I., & Simon, R. (2009). Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses. Virology, 388, 1–7
Kuwata, S., Kubo, S., Yamashita, S., & Doi, Y. (1983). Rod-shaped particles, a probable entity of lettuce big vein virus. Annals of the Phytopathological Society of Japan, 49, 246–251
Land, M., Hauser, L., Jun, S.-R., Nookaew, I., Leuze, M. R., Ahn, T. H., Karpinets, T., Lund, O., Kora, G., Wassenaar, T., Poudel, S., & Ussery, D. W. (2015). Insights from 20 years of bacterial genome sequencing. Functional & Integrative Genomics, 15, 141–161
Leboldus, J. M., Kinzer, K., Richards, J., Ya, Z., Yan, C., Friesen, T. L., & Brueggeman, R. (2015). Genotype-by-sequencing of the plant-pathogenic fungi Pyrenophora teres and Sphaerulina musiva utilizing ion torrent sequence technology. Molecular Plant Pathology, 16, 623–632
Lot, H., Campbell, R. N., Souche, S., Milne, R. G., & Roggero, P. (2002). Transmission by Olpidium brassicae of Mirafiori lettuce virus and lettuce big-vein virus, and their roles in lettuce big-vein etiology. Phytopathology, 92, 288–293
Luvisi, A., Ampatzidis, Y. G., & De Bellis, L. (2016). Plant pathology and information technology: Opportunity for management of disease outbreak and applications in regulation frameworks. Sustainability, 8, 831
Macdiarmid, R., Rodoni, B., Melcher, U., Ochoa-Corona, F., & Roossinck, M. (2013). Biosecurity implications of new technology and discovery in plant virus research. PLoS Pathogens, 9, e1003337
Mahuku, G., Lockhart, B. E., Wanjala, B., Jones, M. W., Kimunye, J. N., Stewart, L. R., Cassone, B. J., Sevgan, S., Nyasani, J. O., Kusia, E., Kumar, P. L., Niblett, C. L., Kiggundu, A., Asea, G., Pappu, H. R., Wangai, A., Prasanna, B. M., & Redinbaugh, M. G. (2015). Maize lethal necrosis (MLN), an emerging threat to maize-based food security in sub-Saharan Africa. Phytopathology, 105, 956–965
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, 1093–1100
Massart, S., Olmos, A., Jijakli, H., & Candresse, T. (2014). Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Research, 188, 90–96
Massart S, Candresse T, Gil J, et al., 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
Mastin, A. J., Van Den Bosch, F., Gottwald, T. R., Chavez, V. A., & Parnell, S. R. (2017). A method of determining where to target surveillance efforts in heterogeneous epidemiological systems. PLoS Computational Biology, 13, e1005712
Mattocks, C. J., Morris, M. A., Matthijs, G., et al. (2010). A standardized framework for the validation and verification of clinical molecular genetic tests. European Journal of Human Genetics, 18, 1276–1288
Mccourt, C. M., Mcart, D. G., Mills, K., et al. (2013). Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS One, 8, e69604
Mumford, R., Macarthur, R., & Boonham, N. (2016). The role and challenges of new diagnostic technology in plant biosecurity. Food Security, 8, 103–109
Nicolaisen, M., West, J. S., Sapkota, R., Canning, G. G., Schoen, C., & Justesen, A. F. (2017). Fungal communities including plant pathogens in near surface air are similar across northwestern Europe. Frontiers in Microbiology, 8, 1729
Oepp/Eppo. (2007). PM 7/84 basic requirements for quality management in plant pest diagnosis laboratories. Bulletin OEPP/EPPO Bulletin, 37, 580–588
Oepp/Eppo. (2014). PM7/98 specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity. Bulletin OEPP/EPPO Bulletin, 44, 117–147
Palacios G, Druce J, Du L, et al., (2008). A new arenavirus in a cluster of fatal transplant-associated diseases. A New England Journal of Medicine, 358, 991–998
Pritchard, L., Humphris, S., Saddler, G. S., Parkinson, N. M., Bertrand, V., Elphinstone, J. G., & Toth, I. K. (2013). Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. Plant Pathology, 62, 587–596
Rodoni, B. (2009). The role of plant biosecurity in preventing and controlling emerging plant virus disease epidemics. Virus Research, 141, 150–157
Roggero, P., Ciuffo, M., Vaira, A. M., Accotto, G. P., Masenga, V., & Milne, R. G. (2000). An Ophiovirus isolated from lettuce with big-vein symptoms. Archives of Virology, 145, 2629–2642
Roossinck, M. J. (2010). Lifestyles of plant viruses. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365, 1899–1905
Roossinck, M. J. (2013). Plant virus ecology. PLoS Pathogens, 9, e1003304
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
Salto-Tellez, M., & Gonzalez De Castro, D. (2014). Next-generation sequencing: A change of paradigm in molecular diagnostic validation. The Journal of Pathology, 234, 5–10
Sapp, M., Harrison, M., Hany, U., Charlton, A., & Thwaites, R. (2015). Comparing the effect of digestate and chemical fertiliser on soil bacteria. Applied Soil Ecology, 86, 1–9
Schumpp O, Dupuis B, Bréchon A, Al. E, (2016). Diagnostic moléculaire à haut debit pour détecter les viroses des plants de pommes de terre. Recherche Agronomique Suisse, 7, 456–465
Skelton A, Uzayisenga B, Fowkes A, et al., (2018). First report of pepper veinal mottle virus, pepper yellows virus and a novel enamovirus in chilli pepper (Capsicum sp.) in Rwanda. New Disease Reports 37, 5
Talbot, N., Mccafferty, H., Ma, M., Moore, K., & Hamer, J. (1997). Nitrogen starvation of the rice blast fungusMagnaporthe griseamay act as an environmental cue for disease symptom expression. Physiological and Molecular Plant Pathology, 50, 179–195
Thompson, R. N., Gilligan, C. A., & Cunniffe, N. J. (2018). Control fast or control smart: When should invading pathogens be controlled? PLoS Computational Biology, 14, e1006014
Verbeek, M., Dullemans, A. M., Van Bekkum, P. J., & Van Der Vlugt, R. A. (2013). Evidence for lettuce big-vein associated virus as the causal agent of a syndrome of necrotic rings and spots in lettuce. Plant Pathology, 62, 444–451
Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C., & Ding, Z. (2012). Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3, 613–623
