Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications

  • Shigehiro KurakuEmail author
  • Axel Meyer
Part of the Methods in Molecular Biology book series (MIMB, volume 855)


Identification of intragenomic conservation of gene compositions in multiple chromosomal segments led to evidence of whole genome (WGDs) duplications. The process by which WGDs have been maintained and decayed provides us with clues for understanding how the genome evolves. In this chapter, we summarize current understanding of phylogenetic distribution and evolutionary impact of WGDs, introduce basic procedures to detect conserved synteny, and discuss typical pitfalls, as well as biological insights.

Key words

Whole genome duplication Conserved synteny Chromosome rearrangement Differential gene loss Hidden paralogy 


  1. 1.
    Van de Peer, Y., Maere, S., Meyer, A. (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet, 10, 725–32.PubMedCrossRefGoogle Scholar
  2. 2.
    Kuraku, S., Meyer, S. (2010) “Whole Genome Duplications and the Radiation of Vertebrates in Evolution after Gene Duplication. Pp. 299–311.” Katharina Dittmar and David Liberles, Eds. Wiley-Blackwell, NY.Google Scholar
  3. 3.
    Ohno, S.: Evolution by gene duplication. New York: Springer-Verlag; 1970.Google Scholar
  4. 4.
    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.PubMedCrossRefGoogle Scholar
  5. 5.
    Holland, P. W., Garcia-Fernandez, J., Williams, N. A., Sidow, A. (1994) Gene duplications and the origins of vertebrate development. Dev. Sppl., 125–133.Google Scholar
  6. 6.
    Sidow, A. (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev, 6, 715–22.PubMedCrossRefGoogle Scholar
  7. 7.
    Endo, T., Imanishi, T., Gojobori, T., Inoko, H. (1997) Evolutionary significance of intra-genome duplications on human chromosomes. Gene, 205, 19–27.PubMedCrossRefGoogle Scholar
  8. 8.
    Kasahara, M., Hayashi, M., Tanaka, K., Inoko, H., Sugaya, K., Ikemura, T., Ishibashi, T. (1996) Chromosomal localization of the proteasome Z subunit gene reveals an ancient chromosomal duplication involving the major histocompatibility complex. Proc Natl Acad Sci U S A, 93, 9096–101.PubMedCrossRefGoogle Scholar
  9. 9.
    Katsanis, N., Fitzgibbon, J., Fisher, E. M. (1996) Paralogy mapping: identification of a region in the human MHC triplicated onto human chromosomes 1 and 9 allows the prediction and isolation of novel PBX and NOTCH loci. Genomics, 35, 101–8.PubMedCrossRefGoogle Scholar
  10. 10.
    Pebusque, M. J., Coulier, F., Birnbaum, D., Pontarotti, P. (1998) Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol Biol Evol, 15, 1145–59.PubMedCrossRefGoogle Scholar
  11. 11.
    Thornton, J. W. (2001) Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions. Proc Natl Acad Sci U S A, 98, 5671–6.PubMedCrossRefGoogle Scholar
  12. 12.
    Kuraku, S., Meyer, A., Kuratani, S. (2009) Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol Biol Evol, 26, 47–59.PubMedCrossRefGoogle Scholar
  13. 13.
    Dehal, P., Boore, J.L. (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol, 3, e314.Google Scholar
  14. 14.
    Meyer, A., 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.PubMedCrossRefGoogle Scholar
  15. 15.
    Meyer, A., Van de Peer, Y. (2005) From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays, 27, 937–45.PubMedCrossRefGoogle Scholar
  16. 16.
    Fawcett, J. A., Maere, S., Van de Peer, Y. (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A, 106, 5737–42.PubMedCrossRefGoogle Scholar
  17. 17.
    Renwick, J. H. (1971) The mapping of human chromosomes. Annu Rev Genet, 5, 81–120.PubMedCrossRefGoogle Scholar
  18. 18.
    Passarge, E., Horsthemke, B., Farber, R. A. (1999) Incorrect use of the term synteny. Nat Genet, 23, 387.PubMedCrossRefGoogle Scholar
  19. 19.
    Hubbard, T. J., Aken, B. L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., et al. (2009) Ensembl 2009. Nucleic Acids Res, 37, D690–7.PubMedCrossRefGoogle Scholar
  20. 20.
    Haider, S., Ballester, B., Smedley, D., Zhang, J., Rice, P., Kasprzyk, A. (2009) BioMart Central Portal – unified access to biological data. Nucleic Acids Res, 37, W23–7.PubMedCrossRefGoogle Scholar
  21. 21.
    Jacobs, G. H. (1993) The distribution and nature of colour vision among the mammals. Biol Rev Camb Philos Soc, 68, 413–71.PubMedCrossRefGoogle Scholar
  22. 22.
    Davies, W. L., Carvalho, L. S., Cowing, J. A., Beazley, L. D., Hunt, D. M., Arrese, C. A. (2007) Visual pigments of the platypus: a novel route to mammalian colour vision. Curr Biol, 17, R161–3.PubMedCrossRefGoogle Scholar
  23. 23.
    Alioto, T. (2012) Gene prediction. In Anisimova, M., (ed.), Evolutionary genomics: statistical and computational methods (volume 1). Methods in Molecular Biology, Springer Science+Business media, LLC.Google Scholar
  24. 24.
    Picardi, E., Pesole, G.: Computational methods for ab Initio and comparative gene finding. In: Data Mining Techniques for the Life Sciences Edited by O Carugo, F Eisenhaber, vol. 609: Springer Verlag; 2010.Google Scholar
  25. 25.
    Stanke, M., Waack, S. (2003) Gene prediction with a Hidden-Markov model and a new intron submodel. Bioinformatics, 19, Suppl. 2, pages ii215-ii225.Google Scholar
  26. 26.
    Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25, 3389–402.PubMedCrossRefGoogle Scholar
  27. 27.
    Wolfe, K. H. (2001) Yesterday’s polyploids and the mystery of diploidization. Nat Rev Genet, 2, 333–41.PubMedCrossRefGoogle Scholar
  28. 28.
    Van de Peer, Y., Meyer, A.: Large-scale gene and ancient genome duplications. In: The Evolution of the Genome Edited by R Gregory: Elsevier; 2005.Google Scholar
  29. 29.
    Altenhoff, A. M., Dessimoz, C. (2012) Inferring orthology and paralogy. In Anisimova, M., (ed.), Evolutionary genomics: statistical and computational methods (volume 1). Methods in Molecular Biology, Springer Science+Business media, LLC.Google Scholar
  30. 30.
    Gabaldon, T. (2008) Large-scale assignment of orthology: back to phylogenetics? Genome Biol, 9, 235.PubMedCrossRefGoogle Scholar
  31. 31.
    Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., Walichiewicz, J. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res, 110, 462–7.PubMedCrossRefGoogle Scholar
  32. 32.
    Simillion, C., Janssens, K., Sterck, L., Van de Peer, Y. (2008) i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics, 24, 127–8.PubMedCrossRefGoogle Scholar
  33. 33.
    Catchen, J. M., Conery, J. S., Postlethwait, J. H. (2009) Automated identification of conserved synteny after whole-genome duplication. Genome Res, 19, 1497–505.PubMedCrossRefGoogle Scholar
  34. 34.
    Muffato, M., Louis, A., Poisnel, C. E., Roest Crollius, H. (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics, 26, 1119–21.PubMedCrossRefGoogle Scholar
  35. 35.
    Aris-Brosou, S., Rodrigue, N. (2012) The essentials of computational molecular evolution. In Anisimova, M., (ed.), Evolutionary genomics: statistical and computational methods (volume 1). Methods in Molecular Biology, Springer Science+Business media, LLC.Google Scholar
  36. 36.
    Kuraku, S., Meyer, A. (2009) The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication. Int J Dev Biol, 53, 765–73.PubMedCrossRefGoogle Scholar
  37. 37.
    Larhammar, D., Lundin, L. G., Hallbook, F. (2002) The human Hox-bearing chromosome regions did arise by block or chromosome (or even genome) duplications. Genome Res, 12, 1910–20.PubMedCrossRefGoogle Scholar
  38. 38.
    Carroll, S. B., Grenier, J. K., Weatherbee, S. D.: From DNA to diversity: molecular genetics and the evolution of animal design. Malden, Mass.: Blackwell Science; 2001.Google Scholar
  39. 39.
    Kusserow, A., Pang, K., Sturm, C., Hrouda, M., Lentfer, J., Schmidt, H. A., Technau, U., von Haeseler, A., Hobmayer, B., Martindale, M. Q., et al (2005) Unexpected complexity of the Wnt gene family in a sea anemone. Nature, 433, 156–60.PubMedCrossRefGoogle Scholar
  40. 40.
    Deonier, R. C., Tavaré, S., Waterman, M. S.: Computational genome analysis: an introduction. New York: Springer; 2005.Google Scholar
  41. 41.
    Furlong, R. F., Holland, P. W. (2002) Were vertebrates octoploid? Philos Trans R Soc Lond B Biol Sci, 357, 531–44.PubMedCrossRefGoogle Scholar
  42. 42.
    Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., Postlethwait, J. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 151, 1531–45.PubMedGoogle Scholar
  43. 43.
    Lynch, M., O’Hely, M., Walsh, B., Force, A. (2001) The probability of preservation of a newly arisen gene duplicate. Genetics, 159, 1789–804.PubMedGoogle Scholar
  44. 44.
    Hughes, T., Ekman, D., Ardawatia, H., Elofsson, A., Liberles, D. A. (2007) Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biol, 8, 213.PubMedCrossRefGoogle Scholar
  45. 45.
    Daubin, V., Gouy, M., Perriere, G. (2001) Bacterial molecular phylogeny using supertree approach. Genome Inform, 12, 155–64.PubMedGoogle Scholar
  46. 46.
    Kuraku, S. (2010) Palaeogenomics of the vertebrate ancestor―impact of hidden paralogy in hagfish and lamprey gene phylogeny. Integr Comp Biol, 50, 124–129.PubMedCrossRefGoogle Scholar
  47. 47.
    Maere, S., De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., Van de Peer, Y. (2005) Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci U S A, 102, 5454–9.PubMedCrossRefGoogle Scholar
  48. 48.
    Dennis, G., Jr., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., Lempicki, R. A. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol, 4, P3.PubMedCrossRefGoogle Scholar
  49. 49.
    Beissbarth, T., Speed, T. P. (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics, 20, 1464–5.PubMedCrossRefGoogle Scholar
  50. 50.
    Al-Shahrour, F., Minguez, P., Tarraga, J., Medina, I., Alloza, E., Montaner, D., Dopazo, J. (2007) FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res, 35, W91–6.PubMedCrossRefGoogle Scholar
  51. 51.
    Lynch, V. J., Wagner, G. P. (2009) Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes. PLoS Genet, 5, e1000349.PubMedCrossRefGoogle Scholar
  52. 52.
    Manousaki, T., Feiner, N., Begemann, G., Meyer, A., Kuraku, S. (2011) Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses. Evol Dev, 13, 448–459.Google Scholar
  53. 53.
    Braasch, I., Volff, J. N., Schartl, M. (2009) The endothelin system: evolution of vertebrate-specific ligand-receptor interactions by three rounds of genome duplication. Mol Biol Evol, 26, 783–99.PubMedCrossRefGoogle Scholar
  54. 54.
    Kuraku, S., Takio, Y., Sugahara, F., Takechi, M., Kuratani, S. (2010) Evolution of oropharyngeal patterning mechanisms involving Dlx and endothelins in vertebrates. Dev Biol, 341, 315–23.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Genome Resource and Analysis UnitRIKEN Center for Developmental BiologyKobeJapan
  2. 2.Department of BiologyUniversity of KonstanzConstanceGermany

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