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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