Table of Contents
International Journal of Evolutionary Biology
Volume 2012, Article ID 970920, 8 pages
http://dx.doi.org/10.1155/2012/970920
Research Article

Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome

1University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
2Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, India
3Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, Haldwani 263139, India

Received 20 March 2012; Revised 11 June 2012; Accepted 5 July 2012

Academic Editor: Frédéric Brunet

Copyright © 2012 P. C. Sharma 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. Y. Kashi and D. G. King, “Simple sequence repeats as advantageous mutators in evolution,” Trends in Genetics, vol. 22, no. 5, pp. 253–259, 2006. View at Publisher · View at Google Scholar · View at Scopus
  2. J. B. W. Wolf, C. Harrod, S. Brunner, S. Salazar, F. Trillmich, and D. Tautz, “Tracing early stages of species differentiation: ecological, morphological and genetic divergence of Galápagos sea lion populations,” BMC Evolutionary Biology, vol. 8, article 150, 2008. View at Publisher · View at Google Scholar · View at Scopus
  3. E. Buschiazzo and N. J. Gemmell, “Conservation of human microsatellites across 450 million years of evolution,” Genome Biology and Evolution, vol. 2, pp. 153–165, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. T. Barbará, C. Palma-Silva, G. M. Paggi, F. Bered, M. F. Fay, and C. Lexer, “Cross-species transfer of nuclear microsatellite markers: potential and limitations,” Molecular Ecology, vol. 16, no. 18, pp. 3759–3767, 2007. View at Publisher · View at Google Scholar · View at Scopus
  5. A. Grover, V. Aishwarya, and P. C. Sharma, “Biased distribution of microsatellite motifs in the rice genome,” Molecular Genetics and Genomics, vol. 277, no. 5, pp. 469–480, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. A. Grover, B. Ramesh, and P. C. Sharma, “Development of microsatellite markers in potato and their transferability in some members of Solanaceae,” Physiology and Molecular Biology of Plants, vol. 15, no. 4, pp. 343–358, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. M. Roorkiwal, A. Grover, and P. C. Sharma, “Genome-wide analysis of conservation and divergence of microsatellites in rice,” Molecular Genetics and Genomics, vol. 282, no. 2, pp. 205–215, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. R. Guyot and B. Keller, “Ancestral genome duplication in rice,” Genome, vol. 47, no. 3, pp. 610–614, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. X. Wang, X. Zhao, J. Zhu, and W. Wu, “Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.),” DNA Research, vol. 12, no. 6, pp. 417–427, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. J. Yu, J. Wang, W. Lin et al., “The genomes of Oryza sativa: a history of duplications,” PLoS Biology, vol. 3, no. 2, article e38, pp. 266–281, 2005. View at Publisher · View at Google Scholar
  11. D. Retelska, E. Beaudoing, C. Notredame, C. V. Jongeneel, and P. Bucher, “Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time,” BMC Genomics, vol. 8, article 398, 2007. View at Publisher · View at Google Scholar · View at Scopus
  12. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar · View at Scopus
  13. M. Brudno, S. Malde, A. Poliakov et al., “Glocal alignment: finding rearrangements during alignment,” Bioinformatics, vol. 19, supplement 1, pp. i54–i62, 2003. View at Publisher · View at Google Scholar · View at Scopus
  14. K. A. Frazer, L. Pachter, A. Poliakov, E. M. Rubin, and I. Dubchak, “VISTA: computational tools for comparative genomics,” Nucleic Acids Research, vol. 32, supplement 2, pp. W273–W279, 2004. 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. P. C. Sharma, A. Grover, and G. Kahl, “Mining microsatellites in eukaryotic genomes,” Trends in Biotechnology, vol. 25, no. 11, pp. 490–498, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. A. Bhargava and F. F. Fuentes, “Mutational dynamics of microsatellites,” Molecular Biotechnology, vol. 44, no. 3, pp. 250–266, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. A. Grover and P. C. Sharma, “Is spatial occurrence of microsatellites in the genome a determinant of their function and dynamics contributing to genome evolution?” Current Science, vol. 100, no. 6, pp. 859–869, 2011. View at Google Scholar · View at Scopus
  19. The Rice Chromosomes 11 and 12 Sequencing Consortia, “The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications,” BMC Biology, vol. 3, article 20, 2005. View at Publisher · View at Google Scholar
  20. J. W. Fondon III and H. R. Garner, “Molecular origins of rapid and continuous morphological evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 52, pp. 18058–18063, 2004. View at Publisher · View at Google Scholar · View at Scopus
  21. J. M. Hancock and M. Simon, “Simple sequence repeats in proteins and their significance for network evolution,” Gene, vol. 345, no. 1, pp. 113–118, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. D. E. Riley and J. N. Krieger, “UTR dinucleotide simple sequence repeat evolution exhibits recurring patterns including regulatory sequence motif replacements,” Gene, vol. 429, no. 1-2, pp. 80–86, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. C. Schlötterer, “Hitchhiking mapping—functional genomics from the population genetics perspective,” Trends in Genetics, vol. 19, no. 1, pp. 32–38, 2003. View at Publisher · View at Google Scholar · View at Scopus
  24. C. Schlötterer, M. Kauer, and D. Dieringer, “Allele excess at neutrally evolving microsatellites and the implications for tests of neutrality,” Proceedings of the Royal Society B Biological Science, vol. 271, no. 1541, pp. 869–874, 2004. View at Publisher · View at Google Scholar · View at Scopus
  25. C. A. Driscoll, M. Menotti-Raymond, G. Nelson, D. Goldstein, and S. J. O'Brien, “Genomic microsatellites as evolutionary chronometers: a test in wild cats,” Genome Research, vol. 12, no. 3, pp. 414–423, 2002. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Brandström and H. Ellegren, “Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias,” Genome Research, vol. 18, no. 6, pp. 881–887, 2008. View at Publisher · View at Google Scholar · View at Scopus
  27. M. Brandström, A. T. Bagshaw, N. J. Gemmell, and H. Ellegren, “The relationship between microsatellite polymorphism and recombination hot spots in the human genome,” Molecular Biology and Evolution, vol. 25, no. 12, pp. 2579–2587, 2008. View at Publisher · View at Google Scholar · View at Scopus