Abstract
Based on fish genomic studies, we review mechanisms of divergence in duplicated genes (paralogs), resulted in small (“subfunctionalization”) or large (“neofunctionalization”) changes in paralogs. Gene divergence occurs due to several processes, such as non-synonymous substitutions, exon-intron structure rearrangement, and alterations in regulatory regions, which cause differential temporal or spatial expression of paralogous gene copies during ontogenesis.
References
Kol’tsov, N.K., Problems of Biology, nos. 9–10 of Sotsialisticheskaya rekonstruktsiya i nauka (Socialist Reconstruction and Science), 1932.
Taylor, J.S., Van de Peer, Y., Braasch, I., et al., Comparative Genomics Provides Evidence for an Ancient Genome Duplication Event in Fish, Philos. Trans. R. Soc. London, Ser. B, 2001, vol. 356, pp.1661–1679.
Taylor, J.S., Braasch, I., Frickey, T., et al., Genome Duplication, a Trait Shared Be 22.000 Species of Ray-Finned Fish, Genome Res., 2003, vol. 13, pp. 382–390.
Hoegg, S., Brinkmann, H., Naylor, J.S., et al., Phylogenetic Timing of the Fish-Specific Duplication Correlates with the Diversification of Teleost Fish, J. Mol. Evol., 2004, vol. 59, pp. 190–203.
Vasil’ev, V.P., Evolyutsionnaya kariologiya ryb (Evolutionary Karyology of Fish), Moscow: Nauka, 1985.
Birshtein, V.Ya., Tsitologicheskie i molekulyarnye aspekty evolyutsii pozvonochnykh zhivotnykh (Cytological and Molecular Aspects of Evolution of Vertebrates), Moscow: Nauka, 1987.
Nelson, J.S., Fishes of the World, Wiley: Hoboken, 2006, 4th ed.
Amores, A., Force, A., Yan, Y.L., et al., Zebrafish hox Clusters and Vertebrate Genome Evolution, Science, 1998, vol. 282, pp. 1711–1714.
Ferrier, D.E., Minguillon, C., Holland, P.W., et al., The Amphioxus hox Cluster: Deuterostome Posterior Flexibility and hox 14, Evol. Dev., 2000, vol. 2, pp. 284–293.
Aparicio, S., Chapman, J., Stupka, E., et al., Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes, Science, 2002, vol. 297, pp. 1301–1310.
Malaga-Trillo, E., Laessing, U., Lang, D.M., et al., Evolution of Duplicated Reggie Genes in Zebrafish and Goldfish, J. Mol. Evol., 2002, vol. 54, pp. 235–245.
Josefowicz, C., McClintock, J., and Prince, V., The Fate of Zebrafish Hox Gene Duplications, J. Struct. Func. Genomics, 2003, vol. 3, pp. 185–194.
McGinnis, W. and Krumlauf, R., Homeobox Genes and Axial Pattering, Cell, 1992, vol. 68, pp. 283–302.
de Rosa, R., Greiner, J.K., Andreeva, T., et al., Hox Genes in Brachiopods and Priapulids and Protostome Evolution, Nature, 1999, vol. 399, pp. 772–776.
Naruse, K., Fukamachi, S., Mitani, H., et al., A Detailed Linkage Map of Medaka Oryzias latipes: Comparative Genomics and Genome Evolution, Genetics, 2000, vol. 154, pp. 1773–1784.
Kmita-Cunise, M., Loosli, F., Bierne, J., et al., Homeobox Genes in the Ribbonworm Lineus sanguineus: Evolutionary Implications, Proc. Natl. Acad. Sci. U.S.A., 1998, vol. 95, pp. 3030–3035.
Kappen, C., Schughart, K., and Ruddle, F.H., Two Steps in the Evolution of Antennapedia-Class Vertebrate Homeobox Genes, Proc. Natl. Acad. Sci. U.S.A., 1989, vol. 86, pp. 5459–5463.
Holland, P.W., Garcia-Fernande, J., and Williams, N.A., Gene Duplications and the Origins of Vertebrate Development, Development, 1994, suppl., pp. 125–133.
Sidow, A., Gen(om)e Duplications in the Evolution of Early Vertebrates, Curr. Opin. Genet. Dev., 1996, vol. 6, pp. 715–722.
Godsave, S., Dekker, E.J., Holling, T., et al., Expression Patterns of Hoxb Genes in the Xenopus Embryo Suggest Roles in Anteroposterior Specification of the Hindbrain and in Dorsoventral Pattering of the Mesoderm, Dev. Biol., 1994, vol. 166, pp. 465–476.
Meyer, A. and Malaga-Trillo, E., Vertebrate Genomics: More Fishy Tales of Hox Genes, Curr. Biol., 1999, vol. 9, R210.
King, D.L., Gillis, J.A., Carlisle, H.R., et al., A Natural Deletion of the HoxC Cluster in Elasmobranch Fishes, Science, 2011, vol. 334, no. 6062, pp. 1517–1521.
Kim, C.B., Amemiya, C., Bailey, W., et al., Hox Cluster Genomics in the Horn Shark, Heterodontus francisci, Proc. Natl. Acad. Sci. U.S.A., 2000, vol. 97, pp. 1655–1660.
Chen, J-M., Chuzhanova, N., Stenson, P.D., et al., Meta-Analysis of Gross Insertions Causing Human Genetic Disease: Novel Mutational Mechanisms and the Role of Replication Slippage, Hum. Mutat., 2005, vol. 25, pp. 207–221.
Kassahn, K.S., Dang, V.T., Wilkins, S.J., et al., Evolution of Gene Function and Regulatory Control after Whole-Genome Duplication: Comparative Analyses in Vertebrates, Genome Res., 2009, vol. 19, pp. 1404–1418.
Force, A., Lynch, M., Pickett, F.B., et al., Preservation of Duplicate Genes by Complementary, Degenerative Mutations, Genetics, 1999, vol. 151, pp. 1531–1545.
Woolfe, A. and Elgar, G., Comparative Genomics Using Fugu Reveals Insight into Regulatory Subfuctionalization, Genome Biol., 2007, vol. 8, R53.
Altschmied, J., Delfgaaw, J., Wilde, B., et al., Subfunctionalization of Duplicate mitf Genes Associated with Differential Degeneration of Alternative Exons in Fish, Genetics, 2002, vol. 161, pp. 259–267.
Yu, W.P., Brenner, S., and Venkatesh, B., Duplication, Degeneration and Subfunctionalization of the Nested Synapsin-Timp Genes in Fugu, Trends Genet., 2003, vol. 19, pp. 180–183.
Myuge, N.S. and Ozernyuk, N.D., Comparative Structural Analysis of Myosin Light Chains and Gene Duplication in Fish, Izv. Akad. Nauk, Ser. Biol., 2006, no. 1, pp. 38–43.
Sharma, M.K., Liu, R-Z., Thisse, C., et al., Hierarchical Subfunctionalization of fabp1a, fabp1b and fabp10 Tissue-Specific Expression May Account for Retention of These Duplicated Genes in Zebrafish (Danio rerio) Genome, FEBS J., 2006, vol. 273, pp. 3216–3229.
Zakhartsev, M., Lucassen, M., Kulishova, L., et al., Differential Expression of Duplicated LDH-A Genes during Temperature Acclimation of Weatherfish Misgurnus fossilis: Functional Consequences for the Enzyme, FEBS J., 2007, vol. 274, pp. 1503–1513.
Tümpel, S., Cambronero, F., Wiedemann, L.M., et al., Evolution of cis Elements in the Differential Expression of Two Hoxa2 Coparalogous Gene in Pufferfish (Tarifugu rubripes), Proc. Natl. Acad. Sci. U.S.A., 2006, vol. 103, pp. 5419–5424.
Martinez-Bardera, J.P., Toresson, H., Da Rocha, S., et al., Cloning and Expression of Three Members of the Zebrafish Bmp Family: Bmp2a, Bmp2b and Bmp4, Gene, 1997, vol. 198, nos. 1–2, pp. 53–59.
Myuge, N.S., Tikhonov, A.I., and Ozernyuk, N.D., Ontogenetic and Phylogenetic Analysis of Myosin Light Chain Proteins from Skeletal Muscles of Loach Misgurnus fossilis, Izv. Akad. Nauk, Ser. Biol., 2005, no. 5, pp. 573–577.
Ozernyuk, N.D., Klyachko, O.S., and Polosukhina, E.S., Acclimation Temperature Affects the Functional and Structural Properties of Lactate Dehydrogenase from Fish (Misgurnus fossilis) Skeletal Muscles, Comp. Biochem. Physiol., 1994, vol. 107B, pp. 141–145.
Pulyakhina, I.V. and Ozernyuk, N.D., Lactate Dehydrogenase from the Tetraploid Weatherfish Misgurnus fossilis during Temperature Adaptation: Determination of Structural Differences in Two Forms of the Enzyme by Molecular Modeling Methods, Biofizika (Moscow), 2011, vol. 56, pp. 609–616.
Weeds, A.G. and Lowey, S., Substructure of the Myosin Molecule, J. Mol. Biol., 1971, vol. 61, pp. 701–725.
Cresko, W.A., Yan, Y.L., Baltus, D.A., et al., Genome Duplication, Subfunction Partitioning, and Lineage Divergence: Sox9 in Stickleback and Zebrafish, Dev. Biol., 2003, vol. 228, pp. 480–489.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © N.D. Ozernyuk, N.S. Myuge, 2013, published in Genetika, 2013, Vol. 49, No. 1, pp. 73–80.
Rights and permissions
About this article
Cite this article
Ozernyuk, N.D., Myuge, N.S. Large-scale genome duplications and paralog divergence in fish. Russ J Genet 49, 63–69 (2013). https://doi.org/10.1134/S1022795413010080
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1022795413010080