Evolution and diversity of fish genomes

Current Opinion in Genetics and Development

Volumn 13, Issue 6, 2003, Pages 588-592

  Venkatesh, Byrappa ^a  

^a INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE RADIATION; FISH GENETICS; GENE DUPLICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; GENOME SIZE; INTRON; MOLECULAR EVOLUTION; NONHUMAN; PLASTICITY; POLYPLOIDY; PRIORITY JOURNAL; REVIEW; TELEOST;

ACTINOPTERYGII; PISCES; TELEOSTEI; VERTEBRATA;

EID: 0345016262     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2003.09.001     Document Type: Review

References (43)

1. Nelson JS: Fishes of the World, edn 3. New York: Wiley & Sons; 1994:600.
2. Kumar S., Hedges S.B. A molecular timescale for vertebrate evolution. Nature. 392:1998;917-920.
3. Maisey JG: Discovering Fossil Fishes. New York: Henry Holt and Company; 1996:223.
4. Aparicio S., Chapman J., Stupka E., Putnam N., Chia J.M., Dehal P., Christoffels A., Rash S., Hoon S., Smit A.et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297:2002;1301-1310 This paper reports the landscape, gene complement and predicted proteome of the Fugu genome, the first fish genome to be sequenced to the 'draft' level. The Fugu genome encodes almost the same number of genes as the human genome; however, nearly 25% of human proteins have no matches to predicted Fugu proteins. This set of genes is thought to have diverged significantly after the split of the mammalian and fish lineages. Chromosomal segments conserved between Fugu and human comprise ~14% of the Fugu genome.
5. Allendorf FW, Thorgaard GH: Tetraploidy and the evolution of Salmonid fishes. In Evolutionary Genetics of Fishes. Edited by Turner BJ. New York: Plenum Press; 1984:1-53.
6. Ferris SD: Tetraploidy and the evolution of the catostomid fishes. In Evolutionary Genetics of Fishes. Edited by Turner BJ. New York: Plenum Press; 1984:55-93.
7. Dasilva C., Hadji H., Ozouf-Costaz C., Nicaud S., Jaillon O., Weissenbach J., Crollius H.R. Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome. Proc. Natl. Acad Sci. USA. 99:2002;13636-13641.
8. Brainerd E.L., Slutz S.S., Hall E.K., Phillis R.W. Patterns of genome size evolution in tetraodontiform fishes. Evolution. 55:2001;2363-2368.
9. Neafsey D.E., Palumbi S.R. Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome Res. 13:2003;821-830 On the basis of a comparison of repetitive elements, deletions and insertions between Fugu and a spiny pufferfish whose genome is twice that of Fugu's, the authors conclude that a bias against large-scale insertions in the Fugu is responsible for further reduction in the genome size of this family of puffers after they diverged from the spiny puffers.
10. Amores A., Force A., Yan Y.L., Joly L., Amemiya C., Fritz A., Ho R.K., Langeland J., Prince V., Wang Y.L.et al. Zebrafish hox clusters and vertebrate genome evolution. Science. 282:1998;1711-1714.
11. Aparicio S., Hawker K., Cottage A., Mikawa Y., Zuo L., Venkatesh B., Chen E., Krumlauf R., Brenner S. Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat. Genet. 16:1997;79-83.
12. Naruse K., Fukamachi S., Mitani H., Kondo M., Matsuoka T., Kondo S., Hanamura N., Morita Y., Hasegawa K., Nishigaki R.et al. A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics. 154:2000;1773-1784.
13. Woods I.G., Kelly P.D., Chu F., Ngo-Hazelett P., Yan Y.L., Huang H., Postlethwait J.H., Talbot W.S. A comparative map of the zebrafish genome. Genome Res. 10:2000;1903-1914.
14. Robinson-Rechavi M., Marchand O., Escriva H., Bardet P., Zelus D., Hughes S., Laudet V. Euteleost fish genomes are characterized by expansion of gene families. Genome Res. 11:2001;781-788.
15. Robinson-Rechavi M., Marchand O., Escriva H., Laudet V. An ancient whole-genome duplication may not have been responsible for the abundance of duplicated fish genes. Curr. Biol. 11:2001;458-459.
16. Chiang E.F., Pai C.I., Wyatt M., Tan Y.L., Postlethwait J., Chung B. Two sox9 genes on duplicate zebrafish chromosomes: expression of similar transcription activators in distinct sites. Dev. Biol. 231:2001;149-163.
17. Chiang E.F., Yan Y.L., Guiguen Y., Postlethwait J., Chung B. Two Cyp19 (P450 aromatase) genes on duplicated zebrafish chromosomes are expressed in ovary or brain. Mol. Biol. Evol. 18:2001;542-550.
18. Lister J.A., Close J., Raible D.W. Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential. Dev. Biol. 237:2001;333-344.
19. + ATPase α subunit gene. Genome Res. 11:2001;1625-1631.
20. Taylor J.S., Van de Peer Y., Braasch I., Meyer A. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos. Trans. R Soc. Lond. B Biol. Sci. 356:2001;1661-1679.
21. Altschmied J., Delfgaauw J., Wilde B., Duschl J., Bouneau L., Volff J.N., Schartl M. Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish. Genetics. 161:2002;259-267.
22. Smith S.F., Snell P., Gruetzner F., Bench A.J., Haaf T., Metcalfe J.A., Green A.R., Elgar G. Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q. Genome Res. 12:2002;776-784.
23. Williams H., Brenner S., Venkatesh B. Identification and analysis of additional copies of the platelet-derived growth factor receptor and colony stimulating factor1 receptor genes in fugu. Gene. 295:2002;255-264.
24. Yu W.P., Brenner S., Venkatesh B. Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu. Trends Genet. 19:2003;180-183.
25. Winkler C., Schafer M., Duschl J., Schartl M., Volff J.N. Functional divergence of two zebrafish midkine growth factors following fish-specific gene duplication. Genome Res. 13:2003;1067-1081 The authors demonstrate that the duplicate midkine genes in zebrafish, which arose as a result of fish-specific large-segmental duplications, have undergone functional divergence and show expression pattern and functions that are distinct from that of the single-copy mammalian midkine gene.
26. Postlethwait J.H., Woods I.G., Ngo-Hazelett P., Yan Y.L., Kelly P.D., Chu F., Huang H., Hill-Force A., Talbot W.S. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10:2000;1890-1902.
27. Taylor J.S., Braasch I., Frickey T., Meyer A., Van de Peer Y. Genome duplication, a trait shared by ~22,000 species of ray-finned fish. Genome Res. 13:2003;382-390 The authors extend their previous work [20] by identifying Fugu orthologs for 22 pairs out of 58 pairs of zebrafish genes and show by phylogenetic analysis that these genes duplicated before the divergence of the Fugu and zebrafish. This indicates that there has been a large-scale gene duplication, or a whole-genome duplication, in the ancestor of Fugu and zebrafish.
28. Meyer A., Schartl M. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr. Opin. Cell Biol. 11:1999;699-704.
29. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155.
30. Lynch M., Force A. The origin of interspecific genomic incompatibility via gene duplication. Am. Nat. 156:2000;590-605.
31. Taylor J.S., Van de Peer Y., Meyer A. Genome duplication, divergent resolution and speciation. Trends Genet. 17:2001;299-301.
32. McClintock J.M., Carlson R., Mann D.M., Prince V.E. Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish Hox paralogue group 1 genes. Development. 128:2001;2471-2484.
33. Cheng C.C., Chen L. Evolution of an antifreeze glycoprotein. Nature. 401:1999;443-444.
34. Verheyen E., Salzburger W., Snoeks J., Meyer A. Origin of the superflock of cichlid fishes from lake Victoria, East Africa. Science. 300:2003;325-329 This study traces the origin of cichlid species in Lake Victoria in East Africa to the geologically older Lake Kivu. On the basis of mitochondrial sequence analysis and geological evidence, the authors show that >500 cichlid species colonizing Lake Victoria evolved during the past 100,000 years.
35. Venkatesh B., Ning Y., Brenner S. Late changes in spliceosomal introns define clades in vertebrate evolution. Proc. Natl. Acad Sci. USA. 96:1999;10267-10271.
36. Roy S.W., Fedorov A., Gilbert W. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc. Natl. Acad Sci. USA. 100:2003;7158-7162.
37. Robinson-Rechavi M., Laudet V. Evolutionary rates of duplicate genes in fish and mammals. Mol. Biol. Evol. 18:2001;681-683.
38. Chan STH, Yeung WSB: Sex control and sex reversal in fish under natural conditions. In Fish Physiology, vol 9B. Edited by Hoar WS, Randall DJ, Donaldson EW. New York: Academic Press; 1983:171-222.
39. •].
40. •] independently identified the medaka gene, dmY (also known as dmrt1Y) as a strong candidate for male sex determination. This is the first sex-determining gene identified in fishes.
41. Kondo M., Nanda I., Hornung U., Asakawa S., Shimizu N., Mitani H., Schmid M., Shima A., Schartl M. Absence of the candidate male sex-determining gene dmrt1b(Y) of medaka from other fish species. Curr. Biol. 13:2003;416-420.
42. Hinegardner R., Rosen D.E. Cellular DNA content and the evolution of teleostean fishes. Am. Nat. 106:1972;621-644.
43. Hinegardner R. The cellular DNA content of sharks, rays and some other fishes. Comp. Biochem. Physiol. 55:1976;367-370.