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International Journal of Evolutionary Biology
Volume 2012 (2012), Article ID 917678, 11 pages
http://dx.doi.org/10.1155/2012/917678
Research Article

Genomic Structure and Evolution of Multigene Families: “Flowers” on the Human Genome

1Center for the Promotion of Integrated Sciences, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan
2Department of Biochemistry and Molecular Biology, Pennsylvania State University, 312 Wartik Laboratory, University Park, PA 16802, USA
3Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima 739-8526, Japan
4Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
5Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan
6The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan

Received 29 December 2011; Revised 6 April 2012; Accepted 9 April 2012

Academic Editor: Hirohisa Kishino

Copyright © 2012 Hie Lim Kim et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. L. Huminiecki and K. H. Wolfe, “Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse,” Genome Research A, vol. 14, no. 10, pp. 1870–1879, 2004. View at Scopus
  2. R. Blekhman, A. Oshlack, and Y. Gilad, “Segmental duplications contribute to gene expression differences between humans and chimpanzees,” Genetics, vol. 182, no. 2, pp. 627–630, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. H. C. Mefford and E. E. Eichler, “Duplication hotspots, rare genomic disorders, and common disease,” Current Opinion in Genetics and Development, vol. 19, no. 3, pp. 196–204, 2009. View at Publisher · View at Google Scholar · View at Scopus
  4. F. J. Ayala and M. Coluzzi, “Chromosome speciation: humans, Drosophila, and mosquitoes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 1, pp. 6535–6542, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. H. Skaletsky, T. Kuroda-Kawaguchi, P. J. Minx et al., “The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes,” Nature, vol. 423, no. 6942, pp. 825–837, 2003. View at Publisher · View at Google Scholar · View at Scopus
  6. B. K. Bhowmick, Y. Satta, and N. Takahata, “The origin and evolution of human ampliconic gene families and ampliconic structure,” Genome Research, vol. 17, no. 4, pp. 441–450, 2007. View at Publisher · View at Google Scholar · View at Scopus
  7. S. Rozen, H. Skaletsky, J. D. Marszalek et al., “Abundant gene conversion between arms of palindromes in human and ape Y chromosomes,” Nature, vol. 423, no. 6942, pp. 873–876, 2003. View at Publisher · View at Google Scholar · View at Scopus
  8. X. She, J. E. Horvath, Z. Jiang et al., “The structure and evolution of centromeric transition regions within the human genome,” Nature, vol. 430, no. 7002, pp. 857–864, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. E. V. Linardopoulou, E. M. Williams, Y. Fan, C. Friedman, J. M. Young, and B. J. Trask, “Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication,” Nature, vol. 437, no. 7055, pp. 94–100, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. Y. Ohtsubo, W. Ikeda-Ohtsubo, Y. Nagata, and M. Tsuda, “GenomeMatcher: a graphical user interface for DNA sequence comparison,” BMC Bioinformatics, vol. 9, article 376, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. S. Böhringer, R. Gödde, D. Böhringer, T. Schulte, and J. T. Epplen, “A software package for drawing ideograms automatically,” Online Journal of Bioinformatics, vol. 1, pp. 51–61, 2002.
  12. G. Song, C.-H. Hsu, C. Riemer et al., “Conversion events in gene clusters,” BMC Evolutionary Biology, vol. 11, article 226, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. A. J. Sharp, R. R. Selzer, J. A. Veltman et al., “Characterization of a recurrent 15q24 microdeletion syndrome,” Human Molecular Genetics, vol. 16, no. 5, pp. 567–572, 2007. View at Publisher · View at Google Scholar · View at Scopus
  14. F. Antonacci, J. M. Kidd, T. Marques-Bonet et al., “Characterization of six human disease-associated inversion polymorphisms,” Human Molecular Genetics, vol. 18, no. 14, pp. 2555–2566, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. L. Zhang, H. H. S. Lu, W. Y. Chung, J. Yang, and W. H. Li, “Patterns of segmental duplication in the human genome,” Molecular Biology and Evolution, vol. 22, no. 1, pp. 135–141, 2005. View at Publisher · View at Google Scholar · View at Scopus
  16. X. She, G. Liu, M. Ventura et al., “A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications,” Genome Research, vol. 16, no. 5, pp. 576–583, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. D. Q. Nguyen, C. Webber, J. Hehir-Kwa, R. Pfundt, J. Veltman, and C. P. Ponting, “Reduced purifying selection prevails over positive selection in human copy number variant evolution,” Genome Research, vol. 18, no. 11, pp. 1711–1723, 2008. View at Publisher · View at Google Scholar · View at Scopus
  18. D. Q. Nguyen, C. Webber, and C. P. Ponting, “Bias of selection on human copy-number variants,” Plos Genetics, vol. 2, no. 2, p. e20, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. P. C. Groot, W. H. Mager, and R. R. Frants, “Interpretation of polymorphic DNA patterns in the human α-amylase multigene family,” Genomics, vol. 10, no. 3, pp. 779–785, 1991. View at Publisher · View at Google Scholar · View at Scopus
  20. G. H. Perry, N. J. Dominy, K. G. Claw et al., “Diet and the evolution of human amylase gene copy number variation,” Nature Genetics, vol. 39, no. 10, pp. 1256–1260, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. R. H. Tukey and C. P. Strassburg, “Human UDP-glucuronosyltransferases: metabolism, expression, and disease,” Annual Review of Pharmacology and Toxicology, vol. 40, pp. 581–616, 2000. View at Publisher · View at Google Scholar · View at Scopus
  22. Q.-H. Gong, J. W. Cho, T. Huang et al., “Thirteen UDPglucuronosyltransferase genes are encoded at the human UGT1 gene complex locus,” Pharmacogenetics, vol. 11, no. 4, pp. 357–368, 2001. View at Publisher · View at Google Scholar · View at Scopus
  23. J. A. Bailey, Z. Gu, R. A. Clark et al., “Recent segmental duplications in the human genome,” Science, vol. 297, no. 5583, pp. 1003–1007, 2002. View at Publisher · View at Google Scholar · View at Scopus
  24. G. M. Cooper, D. A. Nickerson, and E. E. Eichler, “Mutational and selective effects on copy-number variants in the human genome,” Nature Genetics, vol. 39, no. 1, pp. S22–S29, 2007. View at Publisher · View at Google Scholar · View at Scopus
  25. J. M. Chen, D. N. Cooper, N. Chuzhanova, C. Férec, and G. P. Patrinos, “Gene conversion: mechanisms, evolution and human disease,” Nature Reviews Genetics, vol. 8, no. 10, pp. 762–775, 2007. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Nei and A. P. Rooney, “Concerted and birth-and-death evolution of multigene families,” Annual Review of Genetics, vol. 39, pp. 121–152, 2005. View at Publisher · View at Google Scholar · View at Scopus
  27. Y. Katsura and Y. Satta, “Evolutionary history of the cancer immunity antigen MAGE gene family,” Plos ONE, vol. 6, no. 6, Article ID e20365, 2011. View at Publisher · View at Google Scholar · View at Scopus
  28. P. Van der Bruggen, C. Traversari, P. Chomez et al., “A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma,” Science, vol. 254, no. 5038, pp. 1643–1647, 1991. View at Scopus
  29. J. E. Horvath, C. L. Gulden, R. U. Vallente et al., “Punctuated duplication seeding events during the evolution of human chromosome 2p11,” Genome Research, vol. 15, no. 7, pp. 914–927, 2005. View at Publisher · View at Google Scholar · View at Scopus
  30. M. Ventura, F. Antonacci, M. F. Cardone et al., “Evolutionary formation of new centromeres in macaque,” Science, vol. 316, no. 5822, pp. 243–246, 2007. View at Publisher · View at Google Scholar · View at Scopus
  31. M. Lomiento, Z. Jiang, P. D'Addabbo, E. E. Eichler, and M. Rocchi, “Evolutionary-new centromeres preferentially emerge within gene deserts,” Genome Biology, vol. 9, no. 12, article R173, 2008. View at Publisher · View at Google Scholar · View at Scopus