Phylogenetic analysis of the mammalian Hoxc8 non-coding region

Chang-Bae Kim; Cooduvalli S. Shashikant; Kenta Sumiyama; Wayne C.H. Wang; Chris T. Amemiya; Frank H. Ruddle

doi:10.1023/A:1022635623260

Journal of Structural and Functional Genomics

March 2003, Volume 3, Issue 1–4, pp 195–199

Phylogenetic analysis of the mammalian Hoxc8 non-coding region

Authors
Authors and affiliations

Chang-Bae Kim
Cooduvalli S. Shashikant
Kenta Sumiyama
Wayne C.H. Wang
Chris T. Amemiya
Frank H. RuddleEmail author

Article

DOI: 10.1023/A:1022635623260

Cite this article as:: Kim, CB., Shashikant, C.S., Sumiyama, K. et al. J Struct Func Genom (2003) 3: 195. doi:10.1023/A:1022635623260

4 Citations

Abstract

The non-coding intergenic regions of Hox genes are remarkably conserved among mammals. To determine the usefulness of this sequence for phylogenetic comparisons, we sequenced an 800-bp fragment of the Hoxc9–Hoxc8 intergenic region from several species belonging to different mammalian clades. Results obtained from the phylogenetic analysis are congruent with currently accepted mammalian phylogeny. Additionally, we found a TC mini satellite repeat polymorphism unique to felines. This polymorphism may serve as a useful marker to differentiate between mammalian species or as a genetic marker in feline matings. This study demonstrates usefulness of a comparative approach employing non-coding regions of Hox gene complexes.

comparative genomics Hox genes mammalian phylogeny Hox genes mammalian phylogeny

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References

Arnason, U. and Gullberg, A. (1994) Relationship of baleen whales established by cytochrome b gene sequence comparison. Nature, 367, 726-728.Google Scholar
Arnason, U. and Gullberg, A. (1996) Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans. Mol. Biol. Evol., 13, 407-417.Google Scholar
Belting, H.G., Shashikant, C.S. and Ruddle, F.H. (1998) Multiple phases of expression and regulaiton of mouse Hoxc8 during early embryogenesis. J. Exp. Zool., 282, 196-222.Google Scholar
De Jong, W.W. (1998) Molecules remodel the mammalian tree. Trends Ecol. Evol., 13, 270-275.Google Scholar
Felsenstein, J. (1995) PHYLIP (phylogeny inference package). Version 3.5c. Department of Genetics, University of Washington, Seattle.Google Scholar
Janke, A. and Arnason, U. (1997) The complete mitochondrial genome of Alligator mississippiensis and separation between recent archosauria (birds and crocodiles). Mol. Biol. Evol. 14, 1266-1272.Google Scholar
Janke, A., Xu, X. and Arnason, U. (1997) The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria. Proc. Natl. Acad. Sci. USA, 94, 1276-1281.Google Scholar
Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules. In Mammalian Protein Metabolism (Ed. H.N. Munro), Academic Press, New York, pp. 21-132.Google Scholar
Margarit, E., Gullen, A., Rebordosa, C., Vidal-Taboada, J., Sanchez, M., Ballesta, F. and Oliva, R. (1998) Identification of conserved potentially regulatory sequences of the SRY gene from 10 different species of mammals. Biochem. Biophys. Res. Commun., 245, 370-377.Google Scholar
Messenger, S.L. and McGuire, J.A. (1998) Morphological molecules, and phylogenetics of cetaceans. Syst. Biol., 47, 90-124.Google Scholar
Ohland, D.P., Harley, E.H. and Best, P.B. (1995) Systematics of cetaceans using restriction site mapping of mitochondrial DNA. Mol. Phylogenet. Evol., 4, 10-19.Google Scholar
Olsen, G.J., Matsuda, H., Hagstrom, R. and Overbeek, R. (1994) FastDNAml: a tool for construction og phylogenetic trees of DNA sequences using maximum-likelihood. Comput. Appl. Biosci., 10, 41-48.Google Scholar
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425Google Scholar
Shashikant, C.S. and Ruddle, F.H. (1996) Combinations of closely situated cis-acting elements determine tissue-specific patterns and anterior extent of early Hoxc8 expression. Proc. Natl. Acad. Sci. USA, 93, 12364-12369.Google Scholar
Shashikant, C.S., Bieberich, C.J., Belting, H.G., Wang, J.C., Borbely, M.A. and Ruddle, F.H. (1995) Regulation of Hoxc-8 during mouse embryonic development: identification and characterization of critical eleements involved in early neural tube expression. Development, 121, 4339-4347.Google Scholar
Shashikant, C.S., Kim, C.B., Borbely, M.A., Wang, W.C.H. and Ruddle, F.H. (1998) Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element. Proc. Natl. Acad. Sci. USA, 95, 15446-15451.Google Scholar
Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I. and Okada, N. (1997) Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature, 388, 666-670.Google Scholar
Spek, C.A., Bertina, R.M. and Reitsma, P.H. (1998) Identification of evolutionarily invariant sequences in the protein C gene promoter. J. Mol. Evol., 47, 663-669. Springer, M.S., Cleven, G.C., Madsen, O., De Jong, W.W., Waddell, V.G., Amrine, H.M. and Stanhope, M.J. (1997). Endemic African mammals shake the phylogenetic tree. Nature, 388, 61-64.Google Scholar
Sumiyama, K., Kim, C.B. and Ruddle, F.H. (2001) An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships. Genomics, 71, 260-262.Google Scholar
Swofford, D.L. (1998) PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, MA.Google Scholar
X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.Google Scholar
Yamamoto, H., Kudo, T., Masuko, N., Miura, H., Sato, S., Tanaka, M., Tanaka, S., Takeuchi, S., Shibahara, S. and Takeuchi, T. (1992) Phylogeny of regulatory regions of vertebrate tyrosinase genes. Pigment Cell Res., 5, 284-294.Google Scholar

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Authors and Affiliations

Chang-Bae Kim
- 1
Cooduvalli S. Shashikant
- 2
Kenta Sumiyama
- 1
Wayne C.H. Wang
- 2
Chris T. Amemiya
- 3
Frank H. Ruddle
- 1
Email author

1.Department of Molecular, Cellular, and Developmental BiologyYale UniversityNew HavenUSA
2.Genetic Resources CenterKorea Research Institute of Bioscience and BiotechnologyTaejonKorea
3.Department of Dairy and Animal Science, College of Agricultural SciencesThe Pennsylvania State UniversityUniversity ParkUSA
4.Department of Molecular GeneticsVirginia Mason Research CenterSeattleUSA

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Phylogenetic analysis of the mammalian Hoxc8 non-coding region

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