Application of Genome Sequencing in Fisheries and Aquaculture
Yadvesh Ranvir Singh
Dept. of Fish Genetics and Breeding, College of Fisheries, CAU (Imphal), Lembucherra, Tripura (799 210), India
Samikshya Mishra*
Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra (400 061), India
Debiprasad Kantal
Aquatic Environment Management Division, ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra (400 061), India
DOI: NIL
Keywords: Aquaculture, Fisheries, Genome sequencing, Next generation sequencing
Abstract
Genome sequencing is an old yet unexploited avenue in the fisheries sector. It has incorporated around 594 species which is increasing as we are speaking. It has opened the path for taxonomy, selective breeding, conservation, phylogeny, production and sustainable fisheries. It has been done in many fish species of global commercial importance like catla, rohu, puffer fish, zebra fish, atlantic salmon and rainbow trout etc. and many more are still under investigation. Genomics technologies have the flexibility of integration with ‘omics’ approach and other aspects in fisheries sector, with so much potential beyond the current constraints that are preventing aquaculture from reaching its new heights. Still, many more limitations in the current genome sequencing system need to be addressed.
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Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., Gelpke, M.D., Roach, J., Oh, T., Ho, I.Y., Wong, M., Detter, C., Verhoef, F., Predki, P., Tay, A., Lucas, S., Richardson, P., Smith, S.F, Clark, M.S., Edwards, Y.J., Doggett, N., Zharkikh, A., Tavtigian, S.V., Pruss, D., Barnstead, M., Evans, C., Baden, H., Powell, J., Glusman, G., Rowen, L., Hood, L., Tan, Y.H., Elgar, G., Hawkins, T., Venkatesh, B., Rokhsar, D., Brenner, S., 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297(5585), 1301-1310. DOI: https://doi.org/10.1126/science.1072104.
Howe, K., Clark, M.D., Torroja, C., Torrance, J., Berthelot, C., Muffato, M., Collins, J., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Cáccamo, M., Churcher, C., Scott, C., Barrett, J.C., Koch, R., Rauch, G., White, S., Howe, K., Clark, M. D., Torroja, C., Torrance, J., Berthelot, C., Muffato, M., Collins, J., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Cáccamo, M., Churcher, C., Scott, C., Barrett, J.C., Koch, R., Rauch, G.J., White, S., Chow, W., Kilian, B., Quintais, L., Guerra-Assunção, J.A., Zhou, Y., Gu, Y., Yen, J., Vogel, J.H., Eyre, T.A., Redmond, S., Banerjee, R., Chi, J., Fu, B., Langley, E., Maguire, S., Laird, G.K., Lloyd, D.M., Kenyon, E.J., Donaldson, S., Sehra, H., Almeida-King, J., Loveland, J., Trevanion, S.J., Jones, M., Quail, M., Willey, D., Hunt, A., Burton, J.H., Sims, S., McLay, K., Plumb, B., Davis, J., Clee, C., Oliver, K., Clark, R., Riddle, C., Elliott, D., Threadgold, G., Harden, G., Ware, D., Begum, S., Mortimore, B., Kerry, G., Heath, P.D., Phillimore, B., Tracey, A., Corby, N., Dunn, M., Johnson, C.M., Wood, J., Clark, S.Y., Pelan, S., Griffiths, G., Smith, M., Glithero, R., Howden, P., Barker, N., Lloyd, C., Stevens, C., Harley, J., Holt, K., Panagiotidis, G., Lovell, J., Beasley, H., Henderson, C., Gordon, D., Auger, K.A., Wright, D., Collins, J., Raisen, C., Dyer, L., Leung, K., Robertson, L., Ambridge, K., Leongamornlert, D., McGuire, S., Gilderthorp, R., Griffiths, C., Manthravadi, D., Nichol, S., Barker, G., Whitehead, S., Kay, M., Brown, J.Y., Murnane, C., Gray, E., Humphries, M., Sycamore, N., Barker, D., Saunders, D., Wallis, J.M., Babbage, A., Hammond, S., Mashreghi-Mohammadi, M., Barr, L., Martin, S., Wray, P., Ellington, A., Matthews, N., Ellwood, M., Woodmansey, R., Clark, G., Cooper, J.D., Tromans, A., Grafham, D., Skuce, C.D., Pandian, R., Andrews, R., Harrison, E., Kimberley, A.M., Garnett, J., Fosker, N., Hall, R.E., Garner, P., Kelly, D., Bird, C.P., Palmer, S., Gehring, I., Berger, A., Dooley, C.M., Ersan-Ürün, Z., Eser, C., Geiger, H., Geisler, M., Karotki, L., Kirn, A., Konantz, J., Konantz, M., Oberländer, M., Rudolph-Geiger, S., Teucke, M., Lanz, C., Raddatz, G., Osoegawa, K., Zhu, B., Rapp, A., Widaa, S., Langford, C., Yang, F., Schuster, S.C., Carter, N.P., Harrow, J., Ning, Z., Herrero, J., Searle, S., Enright, A.J., Geisler, R., Plasterk, R.H.A., Lee, C., Westerfield, M., De Jong, P.J., Zon, L.I., Postlethwait, J.H., Nüsslein-Volhard, C., Hubbard, T., Crollius, H.R., Rogers, J., Stemple, D.L., 2013. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496(7446), 498-503. DOI: https://doi.org/10.1038/nature12111.
Jaillon, O., Aury, J., Brunet, F., Petit, J., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf−Costaz, C., Bernot, A., Nicaud, S., Jaffe, D.B., Fisher, S., Lutfalla, G., Dossat, C., Ségurens, B., Dasilva, C., Salanoubat, M., Levy, M.A., Boudet, N., Castellano, S., Anthouard, V., Jubin, C., Castelli, V., Katinka, M., Vacherie, B., Biémont, C., Skalli, Z., Cattolico, L., Poulain, J., De Berardinis, V., Cruaud, C., Duprat, S., Brottier, P., Coutanceau, J.P., Gouzy, J., Parra, G., Lardier, G., Chapple, C.E., McKernan, K., McEwan, P., Bosak, S., Kellis, M., Volff, J., Guigó, R., Zody, M.C., Mesirov, J.P., Lindblad-Toh, K., Birren, B.W., Nusbaum, C., Kahn, D., Robinson-Rechavi, M., Laudet, V., Schächter, V., Quétier, F., Saurin, W., Scarpelli, C., Wincker, P., Lander, E.S., Weissenbach, J., Crollius, H.R., 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431(7011), 946-957. DOI: https://doi.org/10.1038/nature03025.
Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qü, W., Ahsan, B., Yamada, T., Nagayasu, Y., Doi, K., Kasai, Y., Jindo, T., Kobayashi, D., Shimada, A., Toyoda, A., Kuroki, Y., Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Asakawa, S., Shimizu, N., Hashimoto, S.I., Yang, J., Lee, Y.J., Matsushima, K., Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S., Ohta, F., Nomoto, H., Nogata, K., Morishita, Endo, T., Shin, I,T., Takeda, H., Morishita, S., Kohara, Y., 2007. The medaka draft genome and insights into vertebrate genome evolution. Nature 447(7145), 714-719. DOI: https://doi.org/10.1038/nature05846.
Lu, G., Luo, M., 2020. Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective. Aquaculture and Fisheries 5(4), 163-173. DOI: https://doi.org/10.1016/j.aaf.2020.05.004.