Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish

Genome Research

Volumn 14, Issue 1, 2004, Pages 1-10

  Amores, Angel ^a   Suzuki, Tohru ^b   Yan, Yi Lin ^a   Pomeroy, Jordan ^a   Singer, Amy ^a   Amemiya, Chris ^c   Postlethwait, John H ^a  

^a UNIVERSITY OF OREGON   (United States)

^b FISHERIES RESEARCH AGENCY   (Japan)

^c BENAROYA RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HOX PROTEIN;

ARTICLE; CONTROLLED STUDY; EMBRYO; EMBRYO DEVELOPMENT; GENE CLUSTER; GENE DUPLICATION; GENE EXPRESSION; GENETIC COMPLEMENTATION; GENETIC DATABASE; GENOMIC IN SITU HYBRIDIZATION; HOX GENE; HYPOTHESIS; JAPAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PUFFER FISH; SPECIES DIFFERENCE; TELEOST; ZEBRA FISH;

ANIMALS; CHICKENS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES; GENES, HOMEOBOX; GENOME; HUMANS; MICE; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; SKATES (FISH); TAKIFUGU;

DANIO RERIO; SPHOEROIDES NEPHELUS; TAKIFUGU; TAKIFUGU RUBRIPES; TELEOSTEI; TETRAODONTIDAE; VERTEBRATA;

EID: 0347135956     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1717804     Document Type: Article

References (82)

1. Ahn, S. and Tanksley, S.D. 1993. Comparative linkage maps of the rice and maize genomes. Proc. Natl. Acad. Sci. 90: 7980-7984.
2. Allendorf, F. and Thorgaard, G. 1984. Tetraploidy and the evolution of salmonid fishes. In Evolutionary genetics of fishes (ed. B.J. Turner), pp. 1-46. Plenum Press, New York.
3. Allendorf, F.W., Utter, F.M., and May, B.P. 1975. Gene duplication within the family Salmonidae: II. Detection and determination of the genetic control of duplicate loci through inheritance studies and the examination of populations. In Isozymes (ed. C.L. Markert), pp. 415-432. Academic Press, New York.
4. Amemiya, C., Amores, A., Ota, G., Mueller, D., Garraty, J., Postlethwait, J., and Litman, G. 2001. Generation of a P1 artificial chromosome library of the Southern pufferfish. Gene 272: 283-289.
5. Amores, A., Force, A., Yan, Y.-L., Joly, L., Amemiya, C., Fritz, A., Ho, R.K., Langel, J., Prince, V., Wang, Y.-L., et al. 1998. Zebrafish hox clusters and vertebrate genome evolution. Science 282: 1711-1714.
6. Aparicio, S. 2000. Vertebrate evolution: Recent perspectives from fish. Trends Genet. 16: 54-56.
7. Aparicio, S., Hawker, K., Cottage, A., Mikawa, Y., Zuo, L., Venkatesh, B., Chen, E., Krumlauf, R., and Brenner, S. 1997. Organization of the Fugu rubripes Hox clusters: Evidence for continuing evolution of vertebrate Hox complexes. Nat. Genet. 16: 79-83.
8. Aparicio, S., Chapman, J., Stupk, 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.
9. Bailey, G.S., Poulter, R.T.M., and Stockwell, P.A. 1978. Gene duplcation in tetraploid fish: Model for gene silencing at unlinked duplicated loci. Proc. Natl. Acad. Sci. 75: 5575-5579.
10. Brainerd, E.L. 1994. Pufferfish inflation: Functional morphology of post cranial structures in Diodon holocanthus (Tetraodontiformes). J. Morphol. 220: 243-261.
11. Brainerd, E.L. and Patek, S.N. 1998. Vertebral column morphology, C-start curvature, and the evolution of mechanical defenses in tetraodontiform fishes. Copeia 4: 971-984.
12. Chiu, C.H., Amemiya, C., Dewar, K., Kim, C.B., Ruddle, F.H., and Wagner, G.P. 2002. Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc. Natl. Acad. Sci. 99: 5492-5497.
13. Clark, A.G. 1994. Invasion and maintenance of a gene duplication. Proc. Natl. Acad. Sci. 91: 2950-2954.
14. 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 genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 9: 960-971.
15. Escriva, H., Manzon, L., Youson, J., and Laudet, V. 2002. Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol. Biol. Evol. 19: 1440-1450.
16. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: 401-410.
17. Ferrier, D.E., Minguillon, C., Holland, P.W., and Garcia-Fernandez, J. 2000. The amphioxus Hox cluster: Deuterostome posterior flexibility and Hox14. Evol. Dev. 2: 284-293.
18. Ferris, S.D. and Whitt, G.S. 1979. Evolution of the differential regulation of duplicate genes after polyploidization. J. Mol. Evol. 12: 267-317.
19. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.-L., and Postlethwait, J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
20. Force, A., Amores, A., and Postlethwait, J.H. 2002. Hox cluster organization in the jawless vertebrate Petromyzon marinus. J. Exp. Zool. 294: 30-46.
21. Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., 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.
22. Haldane, J.B.S. 1933. The part played by recurrent mutation in evolution. Am. Nat. 67: 5-9.
23. Hedges, S.B. 2002. The origin and evolution of model organisms. Nat. Rev. Genet. 3: 838-849.
24. Hedges, S.B. and Kumar, S. 2002. Genomics. Vertebrate genomes compared. Science 297: 1283-1285.
25. Holland, P.W. 1997. Vertebrate evolution: Something fishy about Hox genes. Curr. Biol. 7: 570-572.
26. Holland, P.W., Garcia-Fernàndez, J., Williams, N.A., and Sidow, A. 1994. Gene duplications and the origins of vertebrate development. Dev. Suppl. 125-133.
27. Hughes, A.L. 1994. The evolution of functionally novel proteins after gene duplication. Proc. Roy. Soc. Lond. B 256: 119-124.
28. Hughes, M.K. and Hughes, A.L. 1993. Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10: 1360-1369.
29. Hunter, M.P. and Prince, V.E. 2002. Zebrafish box paralogue group 2 genes function redundantly as selector genes to pattern the second pharyngeal arch. Dev. Biol. 247: 367-389.
30. Irvine, S.Q., Carr, J.L., Bailey, W.J., Kawasaki, K., Shimizu, N., Amemiya, C.T., and Ruddle, F.H. 2002. Genomic analysis of Hox clusters in the sea lamprey Petromyzon marinus. J. Exp. Zool. 294: 47-62.
31. Jungbluth, S., Bell, E., and Lumsden, A. 1999. Specification of distinct motor neuron identities by the singular activities of individual Hox genes. Development 126: 2751-2758.
32. Kim, C.B., Amemiya, C., Bailey, W., Kawasaki, K., Mezey, J., Miller, W., Minoshima, S., Shimizu, N., Wagner, G., and Ruddle, F. 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proc. Natl. Acad. Sci. 97: 1655-1660.
33. Kimura, M. and King, J.L. 1979. Fixation of a deleterious allele at one of two "duplicate" loci by mutation pressure and random drift. Proc. Natl. Acad. Sci. 76: 2858-2861.
34. Koh, E.G.L., Lam, K., Christoffels, A., Erdmann, M.V., Brenner, S., and Venkatesh, B. 2003. Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis. Proc. Natl. Acad. Sci. 100: 1084-1088.
35. Kumazawa, Y., Yamaguchi, M., and Nishida, M. 2000. Mitochondrial molecular clocks and the origin of euteleostean biodiversity: Familial radiation of perciforms may have predated the Cretaceous/tertiary boundary. In The biology of biodiversity (ed. M. Kato,), pp. 35-52. Springer-Verlag, New York.
36. Kurokawa, T., Suzuki, T., Ohta, H., Kagawa, H., Tanaka, H., and Unuma, T. 2002. Expression of pancreatic enzyme genes during the early larval stage of Japanese eel Anguilla japonica. Fisheries Sci. 68: 736-744.
37. Larhammar, D. and Risinger, C. 1994. Molecular genetic aspects of tetraploidy in the common carp Cyprinus carpio. Mol. Phylogenet. Evol. 3: 59-68.
38. Ledje, C., Kim, C.B., and Ruddle, F.H. 2002. Characterization of Hox genes in the Bichir, Polypterus palmas. J. Exp. Zool. 294: 107-111.
39. Li, W.-H. 1980. Rate of gene silencing at duplicate loci: A theoretical study and interpretation of data from tetraploid fishes. Genetics 95: 237-258.
40. Lynch, M. and Conery, J. 2000. The evolutionary fate and consequences of gene duplication. Science 290: 1151-1155.
41. Lynch, M. and Force, A. 2000. The origin of interspecific genomic incompatibility via gene duplication. Amer. Nat. 156: 590-605.
42. Malaga-Trillo, E. and Meyer, A. 2001. Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Amer. Zool. 41: 676-686.
43. McClintock, J.M., Carlson, R., Mann, D.M., and Prince, V.E. 2001. Consequences of Hox gene duplication in the vertebrates: An investigation of the zebrafish Hox paralogue group 1 genes. Development 128: 2471-2484.
44. McClintock, J.M., Kheirbek, M.A., and Prince, V.E. 2002. Knockdown of duplicated zebrafish hoxb1 genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention. Development 129: 2339-2354.
45. Meyer, A. and Malaga-Trillo, E. 1999. Vertebrate genomics: More fishy tales about Hox genes. Curr. Biol. 9: R210-R213.
46. 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.
47. Misof, B.Y. and Wagner, G.P. 1996. Evidence for four Hox clusters in the killifish Fundulus heteroclitus (teleostei). Mol. Phylogenet. Evol. 5: 309-322.
48. Morrison, A., Moroni, M.C., Ariza-McNaughton, L., Krumlauf, R., and Mavilio, F. 1996. In vitro and transgenic analysis of a human HOXD4 retinoid-responsive enhancer. Development 122: 1895-1907.
49. Naruse, K., Fukamachi, S., Mitani, H., Kondo, M., Matsuoka, T., Kondo, S., Hanamura, N., Morita, Y., Hasegawa, K., Nishigaki, R., et al. 2000. A detailed linkage map of medaka, Oryzias latipes. Comparative genomics and genome evolution. Genetics 154: 1773-1784.
50. Nei, M. and Roychoudhury, A.K. 1973. Probability of fixation of nonfunctional genes at duplicate loci. Amer. Nat. 107: 362-372.
51. Nelson, J.S. 1994. Fishes of the world. Wiley-Interscience, New York.
52. Nolte, C., Amores, A., Nagy Kovacs, E., Postlethwait, J., and Featherstone, M. 2003. The role of retinoic acid response element in establishing the anterior neural expression border of Hoxd4 transgenes. Mech. Dev. 120: 325-335.
53. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, New York.
54. Ohta, T. 1988. Time for acquiring new gene by duplication. Proc. Natl. Acad. Sci. 85: 3509-3512.
55. Postlethwait, J., Yan, Y., Gates, M., Horne, S., Amores, A., Brownlie, A., Donovan, A., Egan, E., Force, A., Gong, Z., et al. 1998. Vertebrate genome evolution and the zebrafish gene map. Nat. Genet. 18: 345-349.
56. Postlethwait, J., Amores, A., Yan, G., and Austin, C.A. 2002. Duplication of a portion of human chromosome 20q containing Topoisomerase (Top1) and Snail genes provides evidence on genome expansion and the radiation of teleost fish. In: Aquatic genomics: Steps toward a great future (eds. N. Shimizu et al.), pp. 20-31. Springer-Verlag, Tokyo, Japan.
57. Prince, V. and Lumsden, A. 1994. Hoxa-2 expression in normal transposed rhombomeres: Independent regulation in the neural tube and neural crest. Development 120: 911-923.
58. Prince, V.E., Joly, L., Ekker, M., and Ho, R.K. 1998a. Zebrafish hox genes: Genomic organization and modified colinear expression patterns in the trunk. Development 125: 407-420.
59. Prince, V.E., Moens, C.B., Kimmel, C.B., and Ho, R.K. 1998b. Zebrafish hox genes: Expression in the hindbrain region of wild-type and mutants of the segmentation gene, valentino. Development 125: 393-406.
60. Risinger, C. and Larhammar, D. 1993. Multiple loci for synapse protein SNAP-25 in the tetraploid goldfish. Proc. Natl. Acad. Sci. 90: 10598-10602.
61. Santini, F. and Tyler, J.C. 1999. A new phylogenetic hypothesis for the order Tetraodontiformes (Teleostei, Pisces), with placement of the most fossil basal lineages. Amer. Zool. 39: 10A.
62. Santini, S., Boore, J.L., and Meyer, A. 2003. Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res. 13: 1111-1122.
63. Scemama, J.L., Hunter, M., McCallum, J., Prince, V., and Stellwag, E. 2002. Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci. J. Exp. Zool. 294: 285-299.
64. Snell, E.A., Scemama, J.L., and Stellwag, E.J. 1999. Genomic organization of the Hoxa4-Hoxa10 region from Morone saxatilis: Implications for Hox gene evolution among vertebrates. J. Exp. Zool. 285: 41-49.
65. Stickney, H.L., Schmutz, J., Woods, I.G., Holtzer, C.C., Dickson, M.C., Kelly, P.D., Myers, R.M., and Talbot, W.S. 2002. Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res. 12: 1929-1934.
66. Stoltzfus, A. 1999. On the possibility of constructive neutral evolution. J. Mol. Evol. 49: 169-181.
67. Suzuki, T., Oohara, I., and Kurokawa, T. 1998. Hoxd-4 expression during pharyngeal arch development in flounder (Paralichthys olivaceus) embryos and effects of retinoic acid on expression. Zool. Sci. 15: 57-67.
68. Suzuki, T., Kurokawa, T., Hashimoto, H., and Sugiyama, M. 2002. cDNA sequence and tissue expression of Fugu rubripes prion protein-like: A candidate for the teleost orthologue of tetrapod PrPs. Biochem. Biophys. Res. Common. 294: 912-917.
69. Takahata, N. and Maruyama, T. 1979. Polymorphism and loss of duplicate gene expression: A theoretical study with application to tetraploid fish. Proc. Natl. Acad. Sci. 76: 4521-4525.
70. Taylor, J., Braasch, I., Frickey, T., Meyer, A., and Van De Peer, Y. 2003. Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res. 13: 382-390.
71. Taylor, J.S., van de Peer, Y., Braasch, I., and Meyer, A. 2001. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos. Trans. R Soc. Lond. B 356: 1661-1679.
72. Uyeno, T. and Smith, G.R. 1972. Tetraploid origin of the karyotype of catostomid fishes. Science 175: 644-646.
73. Van de Peer, Y., Taylor, J.S., Braasch, I., and Meyer, A. 2001. The ghost of selection past: Rates of evolution and functional divergence in anciently duplicated genes. J. Mol. Evol. 53: 434-444.
74. Van de Peer, Y., Frickey, T., Taylor, J., 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.
75. van der Hoeven, F., Sordino, P., Fraudeau, N., Izpisua-Belmonte, J.C., and Duboule, D. 1996. Teleost HoxD and HoxA genes: Comparison with tetrapods and functional evolution of the HOXD complex. Mech. Dev. 54: 9-21.
76. Wainwright, P.C. and Turingan, R.G. 1997. Evolution of pufferfish inflation behavior. Evolution 51: 506-518.
77. Wainwright, P.C., Turingan, R.G., and Brainerd, E.L. 1995. Functional morphology of pufferfish inflation: Mechanism of the buccal pump. Copeia 1995: 614-625.
78. Watterson, G.A. 1983. On the time for gene silencing at duplicate loci. Genetics 105: 745-766.
79. White, S. and Doebley, J. 1998. Of genes and genomes and the origin of maize. Trends Genet. 14: 327-332.
80. Wittbrodt, J., Meyer, A., and Schartl, M. 1998. More genes in fish? BioEssays 20: 511-515.
81. Wittkopp, P.J., True, J.R., and Carroll, S.B. 2002. Reciprocal functions of the Drosophila yellow and ebony proteins in the development and evolution of pigment patterns. Development 129: 1849-1858.
82. 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.