Abstract
There is a data revolution in the agriculture that involves the analysis of this data, the development of new models and the application of these models in a practical and simple way. All new technologies allow to process big volumes of data with new mathematical algorithms, checking the information in real time, creating new value standards and changing the conception of agriculture. The aim of this chapter is to show some alternatives for the improvement of the crops using the big data, produced with the new technologies for massive sequencing in two specific examples: microbial massive analysis and molecular breeding.
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References
Acharya, A., Poudel, A., Sah, A. K., Maharjan, D., Tibrewal, S., Mandal, P. K., & Maharjan, D. (2016). Isolation and identification of bacteria from meat processing units of Kathmandu Valley. International Journal of Microbiology and Allied Sciences, 2(3), 33–37.
Bashir, Y., Pradeep-Singh, S., & Kumar-Konwar, B. (2014). Metagenomics: An application based perspective. Chinese Journal of Biology, 2014, 1–7.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335.
Chen, K., & Pachter, L. (2005). Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Computational Biology, 1(2), e24.
Delmont, T. O., Robe, P., Cecillon, S., Clark, I. M., Constancias, F., Simonet, P., et al. (2011). Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology, 77(4), 1314–1324.
Ekblom, R., & Galindo, J. (2011). Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity, 107, 1–15.
Escobar-Zepeda, A., de León, A. V. P., & Sanchez-Flores, A. (2015). The road to metagenomics: From microbiology to DNA sequencing technologies and bioinformatics. Frontiers in Genetics, 6, 1–15.
Garsmeur, O., Droc, G., Antonise, R., Grimwood, J., Potier, B., Aitken, K., Jenkins, J., Martin, G., Charron, C., Hervouet, C., Costet, L., Yahiaoui, N., Healey, A., Sims, D., Cherukuri, Y., Sreedasyam, A., Kilian, A., Chan, A., Van Sluys, M.-A., Swaminathan, K., Town, C., Bergès, H., Simmons, B., Glaszmann, J. C., van der Vossen, E., Henry, R., Schmutz, J., & D’Hont, A. (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications, 9, 2638. https://doi.org/10.1038/s41467-018-05051-5
George, I. Stenuit, B., & Agathos, S. (2010). Application of metagenomics to bioremediation. Metagenomics: Theory, methods and applications (1st ed., pp. 119–140). Norfolk: Caister Academic Press
Glick, B. R. (2014). Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiological Research, 169(1), 30–39.
Huson, D. H., Mitra, S., Weber, N., Ruscheweyh, H. J., & Schuster, S. C. (2011). Integrative analysis of environmental sequences using MEGAN 4. Genome Research, 21(9), 1552–1560.
Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., et al. (2016). A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genetics., 48, 657–666. https://doi.org/10.1038/ng.3565
Kwong, W. K., Engel, P., Koch, H., & Moran, N. A. (2014). Genomics and host specilization of honey bee and bumble bee gut symbionts. Proceedings of the National Academy of Sciences, 111(31), 11509–11514.
Lewin, H. A., Robinson, G. E., Kress, W. J, Baker, W. J., Coddington, J., Crandall, K. A, Durbin, R, Edwards, S. V, Forest, F., Gilbert, M. T. P., Goldstein, M. M, Grigoriev, I. V., Hackett, K. J., Haussler, D., Jarvis, E. D., Johnson, W. E., Patrinos, A., Richards, S., Castilla-Rubio, J. C., van Sluys, M. A., Soltis, P. S., Xu, X., Yang, H., Zhang, G. (2018). Earth biogenome project. Sequencing life for the future of life. In Procedings of the National Academy of Sciences USA, 115(17), 4325–4333
Menzel, P., Ng, K. L., & Krogh, A. (2016). Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications, 7, 11257.
Morgan, X. C., & Huttenhower, C. (2012). Human microbiome analysis. PLoS Computational Biology, 8(12), e1002808.
Nakamura, S., Maeda, N., Miron, I. M., Yoh, M., Izutsu, K., Kataoka, C., et al. (2008). Metagenomic diagnosis of bacterial infections. Emerging Infectious Diseases, 14(11), 1784–1786.
Parker, J., & Chen, J. (2017). Application of next generation sequencing for the detection of human viral pathogens in clinical specimens. Journal of Clinical Virology, 86, 20–26.
Potato Genome Consortium. (2011). Genome sequence and analysis of the tuber crop potato. Nature, 475, 189–197. https://doi.org/10.1038/nature10158
Schäfer, M. O., Genersch, E., Fünfhaus, A., Poppinga, L., Formella, N., Bettin, B., & Karger, A. (2014). Rapid identification of differentially virulent genotypes of Paenibacillus larvae, the causative organism of American foulbrood of honey bees, by whole cell MALDI-TOF mass spectrometry. Veterinary Microbiology, 170(3), 291–297.
Schmieder, R., & Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27(6), 863–864.
Schüürmann, J., Quehl, P., Festel, G., & Jose, J. (2014). Bacterial whole-cell biocatalysts by surface display of enzymes: Toward industrial application. Applied Microbiology and Biotechnology, 98(19), 8031–8046.
Tamaki, H., Wright, C. L., Li, X., Lin, Q., Hwang, C., Wang, S., & Liu, W. T. (2011). Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform. PLoS ONE, 6(9), 1–6.
Thomas, T., Gilbert, J., & Meyer, F. (2012). Metagenomics-a guide from sampling to data analysis. Microbial Informatics and Experimentation, 2(1), 3.
Tieman, D., Guangtao, Z., Resende Jr. Marcio F. R., Tao, L., Cuong, N., Dawn, B., Luis, R. J., Stephanie, O. B. K., Taylor, M., Bo, Z., Hiroki, I., Zhongyuan, L., Josef, F., Itay, Z., Antonio, M., Dani, Z., Antonio, G., Matias, K., Sanwen, H., & Klee, H. (2017). A chemical genetic roadmap to improved tomato flavor. Science, 355(6323), 391–394. https://doi.org/10.1126/science.aal1556
Tomato Genome Consortium. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635–641. https://doi.org/10.1038/nature11119
Velsko, I. M., Frantz, L. A., Herbig, A., Larson, G., & Warinner, C. G. (2018). Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research. Msystems, 3, 1–28.
Whiteley, A. S., Jenkins, S., Waite, I., Kresoje, N., Payne, H., Mullan, B., et al. (2012). Microbial 16S rRNA Ion Tag and community metagenome sequencing using the ion torrent (PGM) platform. Journal of Microbiological Methods, 91(1), 80–88.
Wilke, A., Bischof, J., Gerlach, W., Glass, E., Harrison, T., Keegan, K. P., & Chaterji, S. (2015). The MG-RAST metagenomics database and portal in 2015. Nucleic Acids Research, 44(1), 590–594.
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Thanks to Universidad De la Salle Bajío Campus Campestre and Universidad Autónoma de Querétaro for financial support.
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Campos-Guillén, J. et al. (2021). The Use of Big Data in the Modern Biology: The Case of Agriculture. In: León-Castro, E., Blanco-Mesa, F., Gil-Lafuente, A.M., Merigó, J.M., Kacprzyk, J. (eds) Intelligent and Complex Systems in Economics and Business. Advances in Intelligent Systems and Computing, vol 1249. Springer, Cham. https://doi.org/10.1007/978-3-030-59191-5_10
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