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Reconstructing the Evolutionary History of Complex Human Gene Clusters

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 4955)

Abstract

Clusters of genes that evolved from single progenitors via repeated segmental duplications present significant challenges to the generation of a truly complete human genome sequence. Such clusters can confound both accurate sequence assembly and downstream computational analysis, yet they represent a hotbed of functional innovation, making them of extreme interest. We have developed an algorithm for reconstructing the evolutionary history of gene clusters using only human genomic sequence data. This method allows the tempo of large-scale evolutionary events in human gene clusters to be estimated, which in turn will facilitate primate comparative sequencing studies that will aim to reconstruct their evolutionary history more fully.

Keywords

  • Gene Cluster
  • Duplication Event
  • Tandem Duplication
  • Target Distribution
  • Atomic Boundary

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Ohno, S.: Evolution by Gene Dupplication. Springer, Berlin (1970)

    Google Scholar 

  2. Lupski, J.R.: Genomic rearrangements and sporadic disease. Nat. Genet. 39(7 Suppl), 43–47 (2007)

    CrossRef  Google Scholar 

  3. Lander, E.S., et al.: Initial sequencing and analysis of the human genome. Nature 409(6822), 860–921 (2001)

    CrossRef  Google Scholar 

  4. Wong, K.K., de Leeuw, R.J., Dosanjh, N.S., Kimm, L.R., Cheng, Z., Horsman, D.E., MacAulay, C., Ng, R.T., Brown, C.J., Eichler, E.E., Lam, W.L.: A comprehensive analysis of common copy-number variations in the human genome. Am. J Hum. Genet. 80(1), 91–104 (2007)

    CrossRef  Google Scholar 

  5. International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. Nature 431(7011), 931–935 (2004)

    Google Scholar 

  6. Green, E.D.: Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2(8), 573–573 (2001)

    CrossRef  Google Scholar 

  7. Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W.: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14(4), 708–715 (2004)

    CrossRef  Google Scholar 

  8. Raphael, B., Zhi, D., Tang, H., Pevzner, P.: A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 14(11), 2336–2336 (2004)

    CrossRef  Google Scholar 

  9. Margulies, E.H., et al.: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17(6), 760–764 (2007)

    CrossRef  Google Scholar 

  10. Hou, M.: (unpublished data, 2007)

    Google Scholar 

  11. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., Miller, W.: Human-mouse alignments with BLASTZ. Genome Res. 13(1), 103–107 (2003)

    CrossRef  Google Scholar 

  12. Elemento, O., Gascuel, O., Lefranc, M.P.: Reconstructing the duplication history of tandemly repeated genes. Mol. Biol. Evol. 19(3), 278–278 (2002)

    Google Scholar 

  13. Lajoie, M., Bertrand, D., El-Mabrouk, N., Gascuel, O.: Duplication and inversion history of a tandemly repeated genes family. J Comput. Biol. 14(4), 462–468 (2007)

    CrossRef  MathSciNet  Google Scholar 

  14. Jiang, Z., Tang, H., Ventura, M., Cardone, M.F., Marques-Bonet, T., She, X., Pevzner, P.A., Eichler, E.E.: Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat. Genet. 39(11), 1361–1368 (2007)

    CrossRef  Google Scholar 

  15. Wilson, G.M., Flibotte, S., Missirlis, P.I., Marra, M.A., Jones, S., Thornton, K., Clark, A.G., Holt, R.A.: Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res. 16(2), 173–181 (2006)

    CrossRef  Google Scholar 

  16. Dumas, L., Kim, Y.H., Karimpour-Fard, A., Cox, M., Hopkins, J., Pollack, J.R., Sikela, J.M.: Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res. 17(9), 1266–1267 (2007)

    CrossRef  Google Scholar 

  17. Nadeau, J.H., Taylor, B.A.: Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. USA 81(3), 814–818 (1984)

    CrossRef  Google Scholar 

  18. Liu, J.S.: Monte Carlo Strategies in Scientific Computing. Springer, New York (2001)

    MATH  Google Scholar 

  19. Kuhn, R.M., et al.: The UCSC genome browser database: update 2007. Nucleic Acids Res 35(Database issue), D668–D673 (2007)

    CrossRef  Google Scholar 

  20. Becker, K.G., Barnes, K.C., Bright, T.J., Wang, S.A.: The genetic association database. Nat. Genet. 36(5), 431–432 (2004)

    CrossRef  Google Scholar 

  21. Ma, J.: personal communication (2007)

    Google Scholar 

  22. Hurle, B., Swanson, W., Green, E.D.: Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage. Genome Res. 17(3), 276–276 (2007)

    CrossRef  Google Scholar 

  23. The Rhesus Macaque Genome Sequencing and Analysis Consortium: Evolutionary and biomedical insights from the rhesus macaque genome. Science 316(5822), 222–224 (2007)

    Google Scholar 

  24. Daza-Vamenta, R., Glusman, G., Rowen, L., Guthrie, B., Geraghty, D.E.: Genetic divergence of the rhesus macaque major histocompatibility complex. Genome Res. 14(8), 1501–1505 (2004)

    CrossRef  Google Scholar 

  25. Krebs, K.C., Jin, Z., Rudersdorf, R., Hughes, A.L., O’Connor, D.H.: Unusually high frequency MHC class I alleles in Mauritian origin cynomolgus macaques. J Immunol. 175(8), 5230–5239 (2005)

    Google Scholar 

  26. Smith, M.Z., Fernandez, C.S., Chung, A., Dale, C.J., De Rose, R., Lin, J., Brooks, A.G., Krebs, K.C., Watkins, D.I., O’Connor, D.H., Davenport, M.P., Kent, S.J.: The pigtail macaque MHC class I allele Mane-A*10 presents an immundominant SIV Gag epitope: identification, tetramer development and implications of immune escape and reversion. J Med. Primatol 34(5-6), 282–283 (2005)

    CrossRef  Google Scholar 

  27. Averdam, A., Kuhl, H., Sontag, M., Becker, T., Hughes, A.L., Reinhardt, R., Walter, L.: Genomics and diversity of the common marmoset monkey NK complex. J Immunol. 178(11), 7151–7151 (2007)

    Google Scholar 

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© 2008 Springer-Verlag Berlin Heidelberg

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Zhang, Y., Song, G., Vinař, T., Green, E.D., Siepel, A., Miller, W. (2008). Reconstructing the Evolutionary History of Complex Human Gene Clusters. In: Vingron, M., Wong, L. (eds) Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science(), vol 4955. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-78839-3_4

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  • DOI: https://doi.org/10.1007/978-3-540-78839-3_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-78838-6

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