Springer Protocols: Abstract: 17. Inferring Ancestral Gene Order

17. Inferring Ancestral Gene Order

By: Julian M. Catchen³, John S. Conery³, John H. Postlethwait³

Abstract

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To explain the evolutionary mechanisms by which populations of organisms change over time, it is necessary to first understand the pathways by which genomes have changed over time. Understanding genome evolution requires comparing modern genomes with ancestral genomes, which thus necessitates the reconstruction of those ancestral genomes. This chapter describes automated approaches to infer the nature of ancestral genomes from modern sequenced genomes. Because several rounds of whole genome duplication have punctuated the evolution of animals with backbones, and current methods for ortholog calling do not adequately account for such events, we developed ways to infer the nature of ancestral chromosomes after genome duplication. We apply this method here to reconstruct the ancestors of a specific chromosome in the zebrafish Danio rerio.

Affiliation(s): (3) Department of Computer and Information Science and Institute of Neuroscience, University of Oregon, Eugene, OR

Book Title: Bioinformatics: Data, Sequence Analysis and Evolution

Series: Methods in Molecular Biology | Volume: 452 | Pub. Date: May-01-2008 | Page Range: 365-383 | DOI: 10.1007/978-1-60327-159-2_17

Subject: Bioinformatics

Key Words: Ancestral reconstruction - chromosome evolution - genome duplication - automated workflow

References

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1.	Allende, M. L., Manzanares, M., Tena, J. J., et al. (2006) Cracking the genome's second code: enhancer detection by combined phy-logenetic footprinting and transgenic fish and frog embryos. Methods 39, 212–219.

2.	Tran, T., Havlak, P., Miller, J. (2006) Micro-RNA enrichment among short ‘ultraconserved’ sequences in insects. Nucleic Acids Res 34, e65.

3.	Sauer, T., Shelest, E., Wingender, E. (2006) Evaluating phylogenetic footprinting for human-rodent comparisons. Bioinformatics 22, 430–437.

4.	Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.

5.	Wall, D. P., Fraser, H. B., Hirsh, A. E. (2003) Detecting putative orthologs. Bio-informatics 19, 1710–1711.

6.	Ohno, S. (1970) Evolution by Gene Duplication. Springer-Verlag, New York.

7.	Lundin, L. G. (1993) Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16, 1–19.

8.	Spring, J. (1997) Vertebrate evolution by interspecific hybridization—are we poly-ploid? Fed Eur Biol Soc Lett 400, 2–8.

9.	Dehal, P., Boore, J. L. (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3, e314.

10.	Garcia-Fernàndez, J., Holland, P. W. (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370, 563–66.

11.	Ferrier, D. E., Minguillon, C., Holland, P. W., et al. (2000) The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14. Evol Dev 2, 284–293.

12.	Minguillon, C., Gardenyes, J., Serra, E., et al. (2005) No more than 14: the end of the amphioxus Hox cluster. Int J Biol Sci 1, 19–23.

13.	Powers TP, A. C. (2004) Evidence for a Hox14 paralog group in vertebrates. Curr Biol 14, R183–184.

14.	Koh, E. G., Lam, K., Christoffels, A., et al. (2003) Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis. Proc Natl Acad Sci U S A 100, 1084–1088.

15.	Amores, A., Force, A., Yan, Y.-L., et al. (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711–1714.

16.	Chiu, C. H., Amemiya, C., Dewar, K., et al. (2002) Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc Natl Acad Sci U S A 99, 5492–5497.

17.	Acampora, D., D'Esposito, M., Faiella, A., et al. (1989) The human HOX gene family. Nucleic Acids Res 17, 10385–10402.

18.	Graham, A., Papalopulu, N., Krumlauf, R. (1989) The murine and Drosophila home-obox gene complexes have common features of organization and expression. Cell 57, 367–378.

19.	Duboule, D. (1998) Vertebrate hox gene regulation: clustering and/or colinearity? Curr Opin Genet Dev 8, 514–518.

20.	Postlethwait, J. H., Yan, Y.-L., Gates, M., et al. (1998) Vertebrate genome evolution and the zebrafish gene map. Nat Genet 18, 345–349.

21.	Postlethwait, J. H., Amores, A., Yan, G., et al. (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 (Shimizu, N., Aoki, T., Hirono, I., Takashima, F., eds.), Aquatic Genomics: Steps Toward a Great Future. Springer-Verlag, Tokyo.

22.	Taylor, J., Braasch, I., Frickey, T., et al. (2003) Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res. 13, 382–390.

23.	Van de Peer, Y., Taylor, J. S., Meyer, A. (2003) Are all fishes ancient polyploids? J Struct Funct Genomics 3, 65–73.

24.	Hoegg, S., Brinkmann, H., Taylor, J. S., et al. (2004) Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 59, 190–203.

25.	Amores, A., Suzuki, T., Yan, Y. L., et al. (2004) Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res 14, 1–10.

26.	Hoegg, S., Meyer, A. (2005) Hox clusters as models for vertebrate genome evolution. Trends Genet 21, 421–424.

27.	Naruse, K., Tanaka, M., Mita, K., et al. (2004) A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res 14, 820–828.

28.	Aparicio, S., Hawker, K., Cottage, A., et al. (1997) Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat Genet 16, 79–83.

29.	Hedges, S. B. (2002) The origin and evolution of model organisms. Nat Rev Genet 3, 838–849.

30.	Postlethwait, J. H., Woods, I. G., Ngo-Hazelett, P., et al. (2000) Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 10, 1890–1902.

31.	Jaillon, O., Aury, J. M., Brunet, F., et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946–957.

32.	Conery, J., Catchen, J., Lynch, M. (2005) Rule-based workflow management for bio-informatics. VLDB J 14, 318–329.

33.	Van de Peer, Y. (2004) Computational approaches to unveiling ancient genome duplications. Nat Rev Genet 5, 752–763.

34.	Coulier, F., Popovici, C., Villet, R., et al. (2000) MetaHox gene clusters. J Exp Zool 288, 345–351.

35.	Elgar, G., Clark, M., Green, A., et al. (1997) How good a model is the Fugu genome? Nature 387, 140.

36.	Inoue, J. G., Miya, M., Tsukamoto, K., et al. (2003) Basal actinopterygian relationships: a mitogenomic perspective on the phylog-eny of the “ancient fish”. Mol Phylogenet Evol 26, 110–120.

37.	Miya, M., Takeshima, H., Endo, H., et al. (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26, 121–138.

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