Evidence for four Hox clusters in the Killifish Fundulus heteroditus (Teleostei)

Molecular Phylogenetics and Evolution

Volumn 5, Issue 2, 1996, Pages 309-322

  Misof, Bernhard Y ^a   Wagner, Günter P ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYPRINODONTIFORMES; FUNDULUS HETEROCLITUS; FUNDULUS HETERODITUS; MAMMALIA; TELEOSTEI; VERTEBRATA;

HOMEODOMAIN PROTEIN; PRIMER DNA;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; CYPRINODONTIFORMES; EVOLUTION; FISH; GENETICS; HOMEOBOX; HUMAN; KINETICS; MOLECULAR GENETICS; MOUSE; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PROBABILITY; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; DNA PRIMERS; EVOLUTION; FISHES; GENES, HOMEOBOX; HOMEODOMAIN PROTEINS; HUMANS; KILLIFISHES; KINETICS; MICE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; POLYMERASE CHAIN REACTION; PROBABILITY; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 0030122155     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1996.0026     Document Type: Article

References (60)

1. Akam, M. (1989). Hox and HOM: Homologous gene clusters in insects and vertebrates. Cell 57: 347-349.
2. Averof, M., and Akam, M. (1993). HOM/Hox genes of Artemia: Implications for the origin of the insect and crustacean body plans. Curr. Biol. 3: 73-78.
3. Bartels, J. L., Murtha, M. T., and Ruddle, F. H. (1993). Multiple Hox/ HOM-class homeoboxes in Plathelminthes. Mol. Phylogenet. Evol. 2: 143-151.
4. Beeman, R. W., Stuart, J. J., Brown, S. J., and Denell, R. E. (1993). Structure and function of the homeotic gene complex (HOM-C) in the beetle, Tribolium castaneum. BioEssays 15(7): 439-444.
5. Bogarad, L. D., Utset, M. F., Awgulewitsch, A., Miki, T., Hart, C. P., and Ruddle, F. H. (1989). The developmental expression pattern of a new murine homeobox gene: Hox-2.5. Dev. Biol. 133: 537-549.
6. Bürglin, T. R. (1994). A comprehensive classification of homeobox genes. In "Guidebook to the Homeobox Genes" (D. Duboule, Ed.), pp. 25-71, Oxford Univ. Press, London.
7. Cartwright, P., Dick, M. H., and Buss, L. W. (1993). HOM/Hox type homeoboxes in the chelicerate Limulus polyphemus. Mol. Phylogenet. Evol. 2: 185-192.
8. Chen, T. R., and Ruddle, F. H. (1970). A chromosome study of four species and a hybrid of the kill fish genus Fundulus (Cyprinodontidae). Chromosoma 29: 255-267.
9. Chiarelli, A. B., and Capanna, E. (1973). Checklist of fish chromosomes. In "Cytotaxonomy and Vertebrate Evolution" (A. B. Chiarelli and E. Capanna, Eds.), pp. 205-227, Academic Press, London/ New York.
10. Dick, M. H., and Buss, L. W. (1994). A PCR-based survey of homeobox genes in Ctenodrilus serratus (Annelida: Polychaeta). Mol. Phylogenet. Evol. 3(2): 146-158.
11. Dolecki, G. J., Wannakrairoj, S., Lum, R., Wang, G., Riley, H. D., Carlos, R., Wang, A., and Humphreys, T. (1986). Stage specific expression of a homeo box-containing gene in the non-segmented sea urchin embryo. EMBO J. 5: 925-930.
12. Duboule, D., and Dollé, P. (1989). The structural and functional organization of the murine Hox gene family resembles that of Drosophila homeotic genes. EMBO J. 8: 1497-1505.
13. Eiken, H. G., Njolstad, P. R., Molven, A., and Fjose, A. (1987). A zebrafish homeobox-containing gene with embryonic transcription. Biochem. Biophys. Res. Commun. 149: 1165-1171.
14. Ewens, W. J. (1979). "Mathematical Population Genetics," Springer-Verlag, Berlin, Heidelberg, New York.
15. Fjose, A., Molven, A., and Eiken, H. G. (1988). Molecular cloning and characterization of homeo-box-containing genes from Atlantic salmon. Gene 62: 141-152.
16. Forey, P., and Janvier, P. (1993). Agnathans and the origin of jawed vertebrates. Nature 361: 129-134.
17. Garcia-Fernández, J., and Holland, P. W. H. (1994). Archetypal organization of the amphioxus Hox gene cluster. Nature 370: 563-566.
18. Gehring, W. J., Affolter, M., and Bürglin, T. (1994). Homeodomain proteins. Annu. Rev. Biochem. 63: 487-526.
19. Graham, A., Papalopulu, N., and Krumlauf, R. (1989). The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57: 367-378.
20. Hawkins, N. C., and McGhee, J. D. (1990). Homeobox containing genes in the nematode Caenorhabditis elegans. Nucleic Acids Res. 18: 6101-6106.
21. Holland, P. W. H., Garcia-Fernandez, J., Williams, N. A., and Sidow, A. (1994). Gene duplications and the origins of vertebrate development. Development, Supplement: 125-133.
22. Kappen, C., Schugart, K., and Ruddle, F. H. (1989). Antennapedia class homeobox genes: Organization, expression and evolution. In "Molecular Genetics of Early Drosophila and Mouse Development" (M. R. Capecchi, Ed.), pp. 67-76, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
23. Kappen, C., Schugart, K., and Ruddle, F. H. (1993). Early evolutionary origin of major homeodomain sequence classes. Genomics 18: 54-70.
24. Kaufman, T. C., Lewis, R. A., and Wakimoto, B. T. (1980). Cytogenetic analysis of chromosome 3 in Drosophila melanogaster: The homeotic gene complex in polytene chromosome interval 84A-B. Genetics 94: 115-133.
25. Levine, E., and Schechter, N. (1993). Homeobox genes are expressed in the retina and brain of adult goldfish. Proc. Natl. Acad. Sci. USA 90: 2729-2733.
26. Lewis, E. B. (1978). A gene complex controlling segmentation in Drosophila. Nature 276: 565-570.
27. Maddison, W. P., and Maddison, D. R. (1992). McClade. Analysis of phylogeny and character evolution. Version 3. Sinauer, Sunderland, MA.
28. McClintock Turbeville, J., Schulz, J. R., and Raff, R. A. (1994). Deuterostome phylogeny and the sister group of the chordates: Evidence from molecules and morphology. Mol. Biol. Evol. 11(4): 648-655.
29. McGinnis, W., and Krumlauf, R. (1992). Homeobox genes and axial patterning. Cell 68: 283-302.
30. Miles, A., and Miller, D. J. (1992). Genomes of diploblastic organisms contain homeoboxes: Sequence of eveC, an even-skipped homologue from the cnidarian Acropora formosa. Proc. R. Soc. London B 248: 159-161.
31. Molven, A., Hordvik, I., Njolstad, P. R., Van Ghelue, M., and Fjose, A. (1992). The zebrafish homeobox gene hox(zf-114): Primary structure, expression pattern and evolutionary aspects. Int. J. Dev. Biol. 36: 229-237.
32. Murtha, M. T., Lechman, J. F., and Ruddle, F. H. (1991). Detection of homeobox genes in development and evolution. Proc. Natl. Acad. Sci. USA 88: 10711-10715.
33. Nelson, J. S. (1984). "Fishes of the World," Wiley, New York.
34. Njolstad, P. R., Molven, A., Eiken, H. G., and Fjose, A. (1988a). Structure and neural expression of a zebrafish homeobox sequence. Gene 73: 33-46.
35. Njolstad, P. R., Molven, A., and Fjose, A. (1988b). A zebrafish homologue of the murine Hox-2.1 gene. FEBS Lett. 230: 25-30.
36. Njolstad, P. R., Molven, A., Hordvik, I., Apold, J., and Fjose, A. (1988c). Primary structure, developmentally regulated expression and potential duplication of the zebrafish homeobox gene ZF-21. Nucleic Acids Res. 16: 9097-9111.
37. Njolstad, P., Molven, A., Apold, J., and Fjose, A. (1990). The zebrafish homeobox gene hox-2.2: Transcription unit, potential regulatory regions and in situ localization of transcript. EMBO J. 9: 515-524.
38. Ohno, S. (1970). Evolution by Gene Duplication. Springer-Verlag, Heidelberg.
39. Oliver, G., Vispo, M., Mailhos, A., Martínez, C., Sosa-Pineda, B., Fielitz, W., and Ehrlich, R. (1992). Homeoboxes in flatworms. Gene 121: 337-342.
40. Pavell, A. M., and Stellwag, E. J. (1994). Survey of Hox-like genes in the teleost Morone saxatilis: Implications for evolution of the Hox gene family. Mar. Mol. Biol. Biotechnol. 3(3): 149-157.
41. Pendleton, J. W., Nagai, B. K., Murtha, M. T., and Ruddle, F. H. (1993). Expansion of the Hox gene family and the evolution of chordates. Proc. Natl. Acad. Sci. USA 90: 6300-6304.
42. Potter, C., and Robinson, E. S. (1973). The chromosomes of the cyclostomes. In "Cytotaxonomy and Vertebrate Evolution" (A. B. Chiarelli and E. Capanna, Eds.), pp. 179-203, Academic Press, London, New York.
43. Ruddle, F. H., Bartels, J. L., Bentley, K. L., Kappen, C., Murtha, M. T., and Pendleton, J. W. (1994a). Evolution of Hox Genes. Annu. Rev. Genet. 28: 423-442.
44. Ruddle, F. H., Bentley, K. L., Murtha, M. T., and Risch, N. (1994b). Gene loss and gain in the evolution of vertebrates. Development, Supplement: 155-161.
45. Rundstadler, J. A., and Kocher, T. D. (1991). A new antennapediaclass gene from the zebrafish. Nucleic Acids Res. 19: 5434.
46. Schierwater, B., Murtha, M., Dick, M., Ruddle, F. H., and Buss, L. W. (1991). Homeoboxes in cnidarians. J. Exp. Zool. 260: 413-416.
47. Schugart, K., Kappen, C., and Ruddle, F. H. (1989). Duplication of large genomic regions during the evolution of vertebrate homeobox genes. Proc. Natl. Acad. Sci. USA 86: 7067-7071.
48. Scott, M. P. (1992). Vertebrate homeobox gene nomenclature. Cell 71: 551-553.
49. Seimiya, M., Watanabe, Y., and Kurosawa, Y. (1992). Identification of homeobox-containing genes in the most primitive metazoa, sponge. Zool. Sci. 9: 1213. [Abstract]
50. Shure, M., Wessler, S., and Fedoroff, N. (1986). Molecular identification and isolation of the Waxy locus in maize. Cell 35: 225-233.
51. Smith, G. P. (1994). The progeny of sexual PCR. Nature 370: 324-325.
52. Snow, P., and Buss, L. W. (1994). Antennapedia class homeobox genes from the annelid worm Stylaria lacustris (Annelida: Oligochaeta). Submitted for publication.
53. Stemmer, W. P. C. (1994). DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91: 10747-10751.
54. Stuart, J. J., Brown, S. J., Beeman, R. W., and Denell, R. E. (1991). A deficiency of the homeotic complex of the beetle Tribolium. Nature 350: 72-74.
55. Swofford, D. L. (1993). "PAUP 3.1.1; Phylogentic Analysis Using Parsimony." Champaign, IL, Illinois Natural History Survey.
56. Wagner, A., Blackstone, N., Cartwright, P., Dick, M. H., Misof, B., Snow, P., Wagner, G. P., Bartels, J., Murtha, M. T., and Pendelton, J. (1994). Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst. Biol. 43(2): 250-261.
57. Wagner, A. (1994). Evolution of gene networks by gene duplications: A mathematical model and its implications on genome organization. Proc. Natl. Acad. Sci. USA 91: 4387-4391.
58. Wang, B. B., Müller-Immergluck, M. M., Austin, J., Robinson, N. T., Chisholm, A., and Kenyon, C. (1993). A homeotic gene cluster patterns the anteroposterior body axis of C. elegans. Cell 74: 29-42.
59. Webster, P. J., and Mansour, T. E. (1992). Conserved classes of homeodomains in Schistosoma mansoni, an early bilateral metazoan. Mech. Dev. 38: 25-32.
60. Wilson, R., Ainscough, R., Anderson, K., Baynes, C., Berks, M., Bonfield, J., Burton, J., Conner, M., Copsey, T., Cooper, J., Coulson, A., Craxton, M., Dear, S., Du, Z., Durbin, R., Favello, A., Fraser, A., Fulton, L., Gardner, A., Green, P., Hawkins, T., Hillier, L., Jier, M., Johnston, L., Jones, M., Kershaw, J., Dirsten, J., Laisster, N., Latrelle, P., Lightning, J., Lloyd, C., Mortimore, B., O'Callaghan, M., Parsons, J., Percy, C., Rifken, L., Roopra, A., Saunders, D., Shownkeen, R., Simms, M., Smaldon, N., Smith, A., Smith, M., Sonnhammer, E., Staden, R., Sulston, J., Thierry-Mieg, J., Thomas, K., Vaudin, M., Vaughan, K., Waterston, R., Watson, A., Weinstock, L., Wilkinson-Sproat, J., and Wohldman, P. (1994). 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature 368: 32-38.