Gene Mapping, Discovery, and Expression pp 9-20

Part of the Methods in Molecular Biology book series (MIMB, volume 338)

Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes

  • Razi Khaja
  • Jeffrey R. MacDonald
  • Junjun Zhang
  • Stephen W. Scherer


The aim of this chapter is to provide instruction for analyzing and mapping recent segmental and gene duplications in eukaryotic genomes. We describe a bioinformatics-based approach utilizing computational tools to manage eukaryotic genome sequences to characterize and understand the evolutionary fates and trajectories of duplicated genes. An introduction to bioinformatics tools and programs such as BLAST, Perl, BioPerl, and the GFF specification provides the necessary background to complete this analysis for any eukaryotic genome of interest.

Key Words

Bioinformatics BLAST/MegaBLAST gene duplication gene ontology genome assembly genomic disorder GFF (Generic Feature Format) homology neofunctionalization paralogous Perl/BioPerl pseudogene RefSeq RepeatMasker segmental duplication sequence alignments subfunctionalization 


  1. 1.
    Bailey, J. A., Gu, Z., Clark, R. A., et al. (2002) Recent segmental duplications in the human genome. Science 297, 1003–1007.PubMedCrossRefGoogle Scholar
  2. 2.
    Cheung, J., Estivill, X., Khaja, R., et al. (2003) Genome-wide detection of seg-mental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4, R25.PubMedCrossRefGoogle Scholar
  3. 3.
    Cheung, J., Wilson, M. D., Zhang, J., et al. (2003) Recent segmental and gene dupli-cations in the mouse genome. Genome Biol. 4, R47.PubMedCrossRefGoogle Scholar
  4. 4.
    Bailey, J. A., Church, D. M., Ventura, M., Rocchi, M., and Eichler, E. E. (2004) Analysis of segmental duplications and genome assembly in the mouse. Genome Res. 14, 789–801.PubMedCrossRefGoogle Scholar
  5. 5.
    Tuzun, E., Bailey, J. A., and Eichler, E. E. (2004) Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res. 14, 493–506.PubMedCrossRefGoogle Scholar
  6. 6.
    Lupski, J. R. (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14, 417–422.PubMedCrossRefGoogle Scholar
  7. 7.
    Stankiewicz, P. and Lupski, J. R. (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet. 18, 74–82.PubMedCrossRefGoogle Scholar
  8. 8.
    Eichler, E. E. (2001) Recent duplication, domain accretion and the dynamic muta-tion of the human genome. Trends Genet. 17, 661–669.PubMedCrossRefGoogle Scholar
  9. 9.
    Ji, Y., Eichler, E. E., Schwartz, S., and Nicholls, R. D. (2000) Structure of chromo-somal duplicons and their role in mediating human genomic disorders. Genome Res. 10, 597–610.PubMedCrossRefGoogle Scholar
  10. 10.
    Iafrate, A. J., Feuk, L., Rivera, M. N., et al. (2004) Detection of large-scale varia-tion in the human genome. Nat. Genet. 36, 949–951.PubMedCrossRefGoogle Scholar
  11. 11.
    Armengol, L., Pujana, M. A., Cheung, J., Scherer, S. W., and Estivill, X. (2003) Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum. Mol. Genet. 12, 2201–2208.PubMedCrossRefGoogle Scholar
  12. 12.
    Bailey, J. A., Baertsch, R., Kent, W. J., Haussler, D., and Eichler, E. E. (2004) Hot-spots of mammalian chromosomal evolution. Genome Biol. 5, R23.PubMedCrossRefGoogle Scholar
  13. 13.
    Ohno, S. (1970) Evolution by Gene Duplication. Springer, New York, NY.Google Scholar
  14. 14.
    Buiting, K., Korner, C., Ulrich, B., Wahle, E., and Horsthemke, B. (1999) The human gene for the poly(A)-specific ribonuclease (PARN) maps to 16p13 and has a truncated copy in the Prader-Willi/Angelman syndrome region on 15q11♦ q13. Cytogenet. Cell Genet. 87, 125–131.PubMedCrossRefGoogle Scholar
  15. 15.
    Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.Google Scholar
  16. 16.
    Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7, 203–214.PubMedCrossRefGoogle Scholar
  17. 17.
    Prince, V. E. and Pickett, F. B. (2002) Splitting pairs: the diverging fates of dupli-cated genes. Nat. Rev. Genet. 3, 827–837.PubMedCrossRefGoogle Scholar
  18. 18.
    Ashburner, M., Ball, C. A., Blake, J. A., et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2006

Authors and Affiliations

  • Razi Khaja
    • 1
  • Jeffrey R. MacDonald
    • 1
  • Junjun Zhang
    • 2
  • Stephen W. Scherer
    • 1
  1. 1.Program in Genetics and Genomic Biology, Research InstituteThe Hospital for Sick ChildrenTorontoCanada
  2. 2.The Hospital for Sick ChildrenTorontoCanada

Personalised recommendations