Role of Next Generation Sequencing (NGS) in Plant Disease Management: A Review
DOI:
https://doi.org/10.38211/joarps.2023.04.01.61Keywords:
NGS, Plant, Pathogen, DiagnonisAbstract
A high throughput technique used to determine a part of the nucleotide sequence of an organism’s genome is called next generation sequencing (NGS). NGS has been Proven revolutionary in genomics. Clinical diagnostics, Plant diseases diagnostic and other aspects of medical are now made possible by sequencing. Techniques of NGS: there are different techniques of NGS which are being used in real life sciences i.e., Illumina sequencing, Pyrosequencing, Roche 454 sequencing and Ion torrent sequencing. All vintage methods like culturing in bacterial, fungal, and viral samples are being suppressed by next generation sequencing. The potential for random metagenomic sequencing of sick samples to find potential pathogens has surfaced with the development of next-generation high-throughput parallel sequencing technology. NGS enables highly efficient, rapid, low-cost DNA or RNA high-throughput sequencing of plant virus and viroids genomes, as well as specific small RNAs generated during infection. Although this technique is not so much familiar in the field of plant diseases. However, its widespread application in agronomic sciences will make it possible to create solutions to future food-related challenges that involve biotic stress.
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Ahmadian, A., Ehn, M., & Hober, S. (2006). Pyrosequencing: History, biochemistry and future. Clinica Chimica Acta, 363(1-2), 83-94. DOI: https://doi.org/10.1016/j.cccn.2005.04.038
Alinda, A. K., Okoth, P. K., Onamu, R., David, R., Genevieve, T., & Muoma, J. O. (2020). Next generation sequencing platforms for potato virus hunting, surveillance and discovery. African Journal of Bacteriology Research, 12(1), 1-11.
Angly, F. E., Felts, B., Breitbart, M., Salamon, P., Edwards, R. A., Carlson, C., . . . Rohwer, F. (2006). The marine viromes of four oceanic regions. PLoS Biology, 4, e368. DOI: https://doi.org/10.1371/journal.pbio.0040368
Berg, P. (2014). Fred Sanger: A memorial tribute. Paper presented at the Proceedings of the National Academy of Sciences. DOI: https://doi.org/10.1073/pnas.1323264111
Besnard, G., Jühling, F., Chapuis, E., Zedane, L., Lhuillier, E., Mateille, T., & Bellafiore, S. (2014). Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing. Comptes Rendus Biologies, 337(5), 295-301. DOI: https://doi.org/10.1016/j.crvi.2014.03.003
Breitbart, M., Hewson, I., Felts, B., Mahaffy, J. M., Nulton, J., Salamon, P., & Rohwer, F. (2003). Metagenomic analyses of an uncultured viral community from human feces. Journal of Bacteriology, 185, 6220–6223. DOI: https://doi.org/10.1128/JB.185.20.6220-6223.2003
Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., . . . Geiser, D. M. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder. Science, 318(5848), 283-287. DOI: https://doi.org/10.1126/science.1146498
De Vlaminck, I., Khush, K. K., Strehl, C., Kohli, B., Luikart, H., Neff, N. F., . . . Nicolls, M. R. (2013). Temporal response of the human virome to immunosuppression and antiviral therapy. Cell, 155(5), 1178-1187. DOI: https://doi.org/10.1016/j.cell.2013.10.034
Edwards, R. A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D. M., . . . Rohwer, F. (2006). Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7(1), 1-13. DOI: https://doi.org/10.1186/1471-2164-7-57
Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, C., Jones, R., . . . Rayhawk, S. (2007). Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Applied and Environmental Microbiology, 73(21), 7059-7066. DOI: https://doi.org/10.1128/AEM.00358-07
Guo, J. (2016). Rhizosphere metagenomics of three biofuel crops. USA: Michigan State University.
Holley, R. (1968). Alanine transfer RNA, Nobel lecture.
Kircher, M., Heyn, P., & Kelso, J. (2011). Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics, 12, 1-14. DOI: https://doi.org/10.1186/1471-2164-12-382
Lam, H. Y., Clark, M. J., Chen, R., Chen, R., Natsoulis, G., O'huallachain, M., . . . Gerstein, M. B. (2012). Performance comparison of whole-genome sequencing platforms. Nature Biotechnology, 30(1), 78-82. DOI: https://doi.org/10.1038/nbt.2065
Lecuit, M., & Eloit, M. (2015). The potential of whole genome NGS for infectious disease diagnosis (Vol. 15, pp. 1517-1519): Taylor and Francis. DOI: https://doi.org/10.1586/14737159.2015.1111140
Luo, C., Tsementzi, D., Kyrpides, N., Read, T., & Konstantinidis, K. T. (2012). Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PloS one, 7(2), e30087. DOI: https://doi.org/10.1371/journal.pone.0030087
Mardis, E. R. (2008). Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics, 9, 387-402. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., . . . Chen, Z. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437(7057), 376-380. DOI: https://doi.org/10.1146/annurev.genom.9.081307.164359
Merriman, B., D Team, I. T., & Rothberg, J. M. (2012). Progress in ion torrent semiconductor chip based sequencing. Electrophoresis, 33(23), 3397-3417. DOI: https://doi.org/10.1002/elps.201200424
Meyer, M., & Kircher, M. (2010). Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocols, 2010(6), 5448. DOI: https://doi.org/10.1101/pdb.prot5448
Mwaipopo, B., Rajamäki, M.-L., Ngowi, N., Nchimbi-Msolla, S., Njau, P. J., Valkonen, J. P., & Mbanzibwa, D. R. (2021). Next-generation sequencing-based detection of common bean viruses in wild plants from Tanzania and their mechanical transmission to common bean plants. Plant Disease, 105(9), 2541-2550. DOI: https://doi.org/10.1094/PDIS-07-20-1420-RE
Palacios, G., Druce, J., Du, L., Tran, T., Birch, C., Briese, T., . Marshall, J. (2008). A new arenavirus in a cluster of fatal transplant-associated diseases. New England Journal of Medicine, 358(10), 991-998. DOI: https://doi.org/10.1056/NEJMoa073785
Poudel, R., Jumpponen, A., Schlatter, D. C., Paulitz, T., Gardener, B. M., Kinkel, L. L., & Garrett, K. (2016). Microbiome networks: a systems framework for identifying candidate microbial assemblages for disease management. Phytopathology, 106(10), 1083-1096. DOI: https://doi.org/10.1094/PHYTO-02-16-0058-FI
Quail, M. A., Kozarewa, I., Smith, F., Scally, A., Stephens, P. J., Durbin, R., . . . Turner, D. J. (2008). A large genome center's improvements to the Illumina sequencing system. Nature Methods, 5(12), 1005-1010. DOI: https://doi.org/10.1038/nmeth.1270
Ramirez, K. S., Knight, C. G., de Hollander, M., Brearley, F. Q., Constantinides, B., Cotton, A., . . . de Vries, F. T. (2018). Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature microbiology, 3(2), 189-196. DOI: https://doi.org/10.1038/s41564-017-0062-x
Rothberg, J. M., & Leamon, J. H. (2008). The development and impact of 454 sequencing. Nature Biotechnology, 26(10), 1117-1124. DOI: https://doi.org/10.1038/nbt1485
Simner, P. J., Miller, S., & Carroll, K. C. (2018). Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clinical Infectious Diseases, 66(5), 778-788. DOI: https://doi.org/10.1093/cid/cix881
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R.,. Herndl, G. J. (2006). Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proceedings of the National Academy of Sciences, 103(32), 12115-12120. DOI: https://doi.org/10.1073/pnas.0605127103
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., . . . Smith, H. O. (2004). Environmental genome shotgun sequencing of the Sargasso sea. Science, 304, 66–74. DOI: https://doi.org/10.1126/science.1093857
Williamson, S. J., Rusch, D. B., Yooseph, S., Halpern, A. L., Heidelberg, K. B., Glass, J. I., . Sutton, G. (2008). The Sorcerer II Global Ocean Sampling Expedition: Metagenomic characterization of viruses within aquatic microbial samples. PloS one, 3(1), e1456. DOI: https://doi.org/10.1371/journal.pone.0001456
Yang, S., Johnson, M. A., Hansen, M. A., Bush, E., Li, S., & Vinatzer, B. A. (2022). Metagenomic sequencing for detection and identification of the boxwood blight pathogen Calonectria pseudonaviculata. Scientific reports, 12(1), 1-14. DOI: https://doi.org/10.1038/s41598-022-05381-x
Zhang, T., Breitbart, M., Lee, W. H., Run, J.-Q., Wei, C. L., Soh, S. W. L., . Ruan, Y. (2006). RNA viral community in human feces: Prevalence of plant pathogenic viruses. PLoS Biology, 4(1), e3. DOI: https://doi.org/10.1371/journal.pbio.0040003
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Copyright (c) 2023 Muhammad Saeed, Zainab Jamil, Tayyab Shehzad, Syed Zia ul Hasan, Riffat Bibi, Safia Naureen Malik, Raees Ahmed
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