Genome duplication, a trait shared by 22,000 species of ray-finned fish

Genome Research

Volumn 13, Issue 3, 2003, Pages 382-390

  Taylor, John S ^a,b   Braasch, Ingo ^a   Frickey, Tancred ^a   Meyer, Axel ^a   Van de Peer, Yves ^c  

^a UNIVERSITY OF KONSTANZ   (Germany)

^b UNIVERSITY OF VICTORIA   (Canada)

^c DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHICKEN; CONTROLLED STUDY; FISH; GENE DUPLICATION; GENE IDENTIFICATION; GENE MAPPING; GENETIC LINKAGE; GENOME ANALYSIS; HUMAN; MOUSE; NONHUMAN; ORTHOLOGY; PARALOGY; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; PUFFER FISH; RANDOMIZATION; SPECIES DIFFERENCE; SYNTENY; TETRAPLOIDY; XENOPUS LAEVIS; ZEBRA FISH;

ANIMALS; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES; GENOME; GENOME, HUMAN; HUMANS; MULTIFACTORIAL INHERITANCE; PHENOTYPE; PHYLOGENY; SYNTENY; TAKIFUGU; ZEBRAFISH;

ACTINOPTERYGII; ANURA; DANIO RERIO; GALLUS GALLUS; TAKIFUGU RUBRIPES; TETRAODONTIDAE; XENOPUS LAEVIS;

EID: 0037351989     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.640303     Document Type: Article

References (60)

1. Allendorf, F.W. 1978. Protein polymorphism and the rate of loss of duplicate gene expression. Nature 272: 76-78.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. Amores, A., Force, A., Yan, Y.-L., Joly, L., Amemiya, C., Frity, A., Ho, R.K., Langeland, J., Prince, V., Wang, Y.-L., et al. 1998. Zebrafish hox clusters and vertebrate genome evolution. Science 282: 1711-1714.
4. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
5. Arratia, G. 1997. The monophyly of Teleostei and stem-group teleosts. Consensus and disagreements. In Mesozoic fishes 2 - systematics and fossil record. (eds. G. Arratia and H.-P. Schultze), pp. 265-334. Verlag Dr. Friedrich Pfeil, München, Germany.
6. Bailey, G.S., Poulter, R.T., and Stockwell, P.A. 1978. Gene duplication in tetraploid fish: Model for gene silencing at unlinked duplicated loci. Proc. Natl. Acad. Sci. 11: 5575-5579.
7. Barbazuk, W.B., Korf, I., Kadavi, C., Heyen, J., Tate, S., Wun, E., Bedell, J.A., McPherson, J.D., and Johnson, S.L. 2000. The syntenic relationship of the zebrafish and human genomes. Genome Res. 10: 1351-1358.
8. Cheng, C.-H. C., and Chen, L. 1999. Evolution of an antifreeze glycoprotein. Nature 401: 443-444.
9. Dayhoff, M. 1978. Atlas of Protein Sequence and Structure, Vol 5, Suppl. 3, pp. 345-358. National Biomedical Research Foundation, Washington D.C.
10. Dulai, K.S., von Dornum, M., Mollon, J.D., and Hunt, D.M. 1999. The evolution of trichromatic colour vision by opsin gene duplication in New World and Old World primates. Genome Res. 9: 629-638.
11. Elgar, G., Clark, M.S., Meek, S., Smith, S., Warner, S., Edwards, Y.J.K., Bouchireb, N., Cottage, A., Yeo, G.S.H., Umrania, Y., et al. 1999. Generation and analysis of 25 Mb of genomics DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 9: 960-971.
12. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: 401-410.
13. Ferris, S.D. and Whitt G.S. 1977. Loss of duplicate gene expression after polyploidization. Nature 265: 258-260.
14. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.-I., and Postlethwait, J. 1999. The preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
15. Friedman R. and Hughes, A.L. 2001. Pattern and timing of gene duplication in animal genomes. Genome Res. 11: 1842-1847.
16. Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A., and Talbot, W.S. 1999. A genetic linkage map for zebrafish: Comparative analysis and localization of genes and expressed sequences. Genome Res. 9: 334-347.
17. Goff, S.A., Ricke, D., Lan, T.-H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
18. Gu X. and Huang, W. 2002. Testing the parsimony test of genome duplications: A Counter example. Genome Res. 12: 1-2.
19. Hall, T.A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41: 95-98.
20. Jorden, I.K., Makarova, K.S., Spouge, J.L., Wolf, Y.I., and Koonin, E.V. 2001. Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Res. 11: 555-565.
21. Kishino, S. and Hasegawa, M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29: 170-179.
22. Kwok, C., Korn, R.M., Davis, M.E., Burt, D.W., Critcher, R., McCarthy, L., Paw, B.H., Zon, L.I., Goodfellow, P.N., and Schmitt, K. 1998. Characterization of whole genome radiation hybrid mapping resources for non-mammalian vertebrates. Nucleic Acids Res. 26: 3562-3566.
23. Li, W-H. 1980. Rate of gene silencing at duplicated loci: A theoretical study and interpretation of data from tetraploid fishes. Genetics 95: 237-258.
24. Liu, T. X., Kanki, J. P., Deng, M., Rhodes, J., Yang, H.W., Sheng, X.M., Zon, L.I., and Look, A.T. 2002. Evolutionary conservation of zebrafish linkage group 14 with frequently deleted regions of human chromosome 5 in myeloid malignancies. Proc. Natl. Acad. Sci. 99: 6136-6141.
25. Ludwig, A., Belifiore, N.M., Pitra, C., Svirsky, V., and Jenneckens, I. 2001. Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus). Genetics 158: 1203-1215.
26. Lynch, M. 2001. The molecular natural history of the human genome. Trends Ecol. Evol. 16: 420-422.
27. Lynch, M. and Conery, J.S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
28. Lynch, M. and Force, A.G. 2000. The origin of interspecific genomic incompatibility via gene duplication. Am. Nat. 156: 590-605.
29. Meyer, A. and Schartl, M. 1999. 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: 699-704.
30. Nelson, J.S. 1994. Fishes of the world, 3rd ed. Wiley & Sons, New York, NY.
31. Ohno, S. 1970. Evolution by gene duplication. Spinger-Verlag, New York, NY.
32. Postlethwait, J.H., Woods, I.G., Ngo-Hazelett, P., Yan, Y.-L., Kelly, P.D., Chu, F., Huang, H., Hill-Force, A., and Talbot, W.S. 2000. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10: 1890-1902.
33. Prince, V.E., Joly, L., Ekker, M., and Ho, R.K. 1998. Zebrafish hox genes: Genomics organization and modified colinear expression patterns in the trunk. Development 125: 407-420.
34. Riehle, M.M., Bennette, A.F., and Long A.D. 2001. Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl. Acad. Sci. 98: 525-530.
35. Robinson-Rechavi, M., Marchand, O., Escriva H., and Laudet, V. 2001. An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes. Curr. Biol. 11: R458-R459.
36. Saitou, N. and Nei, M. 1987. The neighbor-joining methods: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
37. Schmidtke, J., Schmitt, E., Matzke, E., and Engel, W. 1979. Non-repetitive DNA sequence divergence in phylogenetically diploid and tetraploid teleostean species of the family Cyprinidae and the order Isopondyli. Chromosoma 75: 185-198.
38. Spring, J. 1997. Vertebrate evolution by interspecific hybridization - are we polyploid? FEBS Lett. 400: 2-8.
39. Stephens, S.G. 1951. Possible significance of duplications in evolution. Adv. Genet. 4: 247-265.
40. Stock, D.W., Quattro, J.M., Whitt, G.S., and Powers, D.A. 1997. Lactate dehydrogenase (LDH) gene duplication during chordate evolution: The cDNA sequence of LDH of the tunicate Styela plicata. Mol. Biol. Evol. 14: 1273-1284.
41. Strimmer, K. and Von Haeseler, A. 1996. Quartet puzzling: A quartet maximum likelihood methods for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.
42. Taylor, J.S., Van de Peer, Y., Braasch, I., and Meyer, A. 2001a. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos. Trans. R. Soc. 356: 1661-1679.
43. Taylor, J.S., Van de Peer, Y., and Meyer A. 2001b. Revisiting recent challenges to the ancient fish-specific genome duplication hypothesis. Curr. Biol. 11: R1005-1007.
44. Taylor, J.S., Van de Peer, Y., and Meyer A. 2001c. Genome duplication, divergent resolution and speciation. Trends Genet. 17: 299-301.
45. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The Clustalwindows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
46. Uyeno, T. and Smith G.R. 1972. Tetraploid origin of the karyotype of catastomid fishes. Science 175: 644-646.
47. Valente Samonte, R. and Eichler, E. 2002. Segmental duplications and the evolution of the primate genome. Nat. Genet. Rev. 3: 65-72.
48. Van de Peer, Y. and De Wachter, Y. 1994. TREECON for Windows: A software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10: 569-570.
49. Van de Peer, Y., Frickey, T., Taylor, J.S., and Meyer, A. 2002. Dealing with saturation at the amino acid level: A case study based on anciently duplicated zebrafish genes. Gene 295: 205-211.
50. Vision, T.J., Brown, D.G., and Tanksley, S.D. 2000. The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
51. Wang, Y. and Gu, X. 2000. Evolution patterns of gene families generated in the early stages of vertebrates. J. Mol Evol. 51: 88-96.
52. Werth, C.R. and Windham, M.D. 1991. A model for divergent, allopatric speciation of polyploidy pteridophytes resulting from silencing of duplicate-gene expression. Am. Nat. 137: 515-526.
53. Westerfield, M. 1993. The zebrafish book. University of Oregon Press, Eugene, OR.
54. Wittbrodt, J., Meyer, A., and Schartl, M. 1998. More genes in fish? Bioessays 20: 511-512.
55. Wittbrodt, J., Shima, A., and Schartl, M. 2002. Medaka - a model organism from the far east. Nat. Genet. Rev. 3: 53-64.
56. Wolfe, K.H. 2001. Yesterday's polyploids and the mystery of diploidization. Nat. Genet. Rev. 2: 333-341.
57. Wolfe K.H. and Shields, D.C. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
58. Woods, I.G., Kelly, P.D., Chu F., Ngo-Hazelett, P., Yan, Y.-L., Huang, H., Postlethwait, J.H., and Talbot, W.S. 2000. A comparative map of the zebrafish genome. Genome Res. 10: 1903-1914.
59. Yu, W.P., Pallen, C.J., Tay, A., Jirik, F.R., Brenner, S., Tan, Y.H., and Venkatesh, B. 2001. Conserved synteny between the Fugu and human PTEN locus and the evolutionary conservation of vertebrate PTEN function. Oncogene 20: 5554-5561.
60. Zhang, J., Zhang, Y.-p., and Rosenberg, H.F. 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30: 411-415.