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Comparative and Functional Genomics
Volume 2009, Article ID 510270, 5 pages
http://dx.doi.org/10.1155/2009/510270
Research Article

Evidence of Extensive Homologous Recombination in the Core Genome of Rickettsia

1Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325035, China
2Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, PA 16802, USA

Received 3 February 2009; Accepted 11 April 2009

Academic Editor: James Thomas

Copyright © 2009 Jinyu Wu 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. Vitorino, I. M. Chelo, F. Bacellar, and L. Zé-Zé, “Rickettsiae phylogeny: a multigenic approach,” Microbiology, vol. 153, part 1, pp. 160–168, 2007. View at Publisher · View at Google Scholar
  2. M. J. Pallen and B. W. Wren, “Bacterial pathogenomics,” Nature, vol. 449, no. 7164, pp. 835–842, 2007. View at Publisher · View at Google Scholar
  3. C. Fraser, W. P. Hanage, and B. G. Spratt, “Recombination and the nature of bacterial speciation,” Science, vol. 315, no. 5811, pp. 476–480, 2007. View at Publisher · View at Google Scholar
  4. B. Mau, J. D. Glasner, A. E. Darling, and N. T. Perna, “Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli,” Genome Biology, vol. 7, no. 5, article R44, pp. 1–12, 2006. View at Publisher · View at Google Scholar
  5. E. Krzywinska, J. Krzywinski, and J. S. Schorey, “Naturally occurring horizontal gene transfer and homologous recombination in Mycobacterium,” Microbiology, vol. 150, part 6, pp. 1707–1712, 2004. View at Publisher · View at Google Scholar
  6. S. Suerbaum, J. M. Smith, K. Bapumia et al., “Free recombination within Helicobacter pylori,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 21, pp. 12619–12624, 1998. View at Publisher · View at Google Scholar
  7. T. Lefébure and M. J. Stanhope, “Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition,” Genome Biology, vol. 8, no. 5, article R71, pp. 1–17, 2007. View at Publisher · View at Google Scholar
  8. V. Daubin, N. A. Moran, and H. Ochman, “Phylogenetics and the cohesion of bacterial genomes,” Science, vol. 301, no. 5634, pp. 829–832, 2003. View at Publisher · View at Google Scholar
  9. E. Lerat, V. Daubin, H. Ochman, and N. A. Moran, “Evolutionary origins of genomic repertoires in bacteria,” PLoS Biology, vol. 3, no. 5, article e130, pp. 1–8, 2005. View at Publisher · View at Google Scholar
  10. L. Baldo, S. Bordenstein, J. J. Wernegreen, and J. H. Werren, “Widespread recombination throughout Wolbachia genomes,” Molecular Biology and Evolution, vol. 23, no. 2, pp. 437–449, 2006. View at Publisher · View at Google Scholar
  11. J. P. Gomes, W. J. Bruno, A. Nunes et al., “Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots,” Genome Research, vol. 17, no. 1, pp. 50–60, 2007. View at Publisher · View at Google Scholar
  12. G. Blanc, H. Ogata, C. Robert et al., “Reductive genome evolution from the mother of Rickettsia,” PLoS Genetics, vol. 3, no. 1, article e14, pp. 1–12, 2007. View at Publisher · View at Google Scholar
  13. F. M. Jiggins, “Adaptive evolution and recombination of Rickettsia antigens,” Journal of Molecular Evolution, vol. 62, no. 1, pp. 99–110, 2006. View at Publisher · View at Google Scholar
  14. F. Chen, A. J. Mackey, J. K. Vermunt, and D. S. Roos, “Assessing performance of orthology detection strategies applied to eukaryotic genomes,” PLoS ONE, vol. 2, no. 4, article e383, pp. 1–12, 2007. View at Publisher · View at Google Scholar
  15. X. Xu, J. Wu, J. Xiao et al., “PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families,” Bioinformatics, vol. 24, no. 9, pp. 1217–1220, 2008. View at Publisher · View at Google Scholar
  16. J. Wu, S. Wang, J. Bai et al., “ArchaeaTF: an integrated database of putative transcription factors in Archaea,” Genomics, vol. 91, no. 1, pp. 102–107, 2008. View at Publisher · View at Google Scholar
  17. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Publisher · View at Google Scholar
  18. S. A. Olson, “EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite,” Briefings in Bioinformatics, vol. 3, no. 1, pp. 87–91, 2002. View at Publisher · View at Google Scholar
  19. P. Simmonds and S. Midgley, “Recombination in the genesis and evolution of hepatitis B virus genotypes,” Journal of Virology, vol. 79, no. 24, pp. 15467–15476, 2005. View at Publisher · View at Google Scholar
  20. D. Bryant and V. Moulton, “Neighbor-net: an agglomerative method for the construction of phylogenetic networks,” Molecular Biology and Evolution, vol. 21, no. 2, pp. 255–265, 2004. View at Publisher · View at Google Scholar
  21. T. H. Kloepper and D. H. Huson, “Drawing explicit phylogenetic networks and their integration into SplitsTree,” BMC Evolutionary Biology, vol. 8, article 22, pp. 1–7, 2008. View at Publisher · View at Google Scholar
  22. D. Martin and E. Rybicki, “RDP: detection of recombination amongst aligned sequences,” Bioinformatics, vol. 16, no. 6, pp. 562–563, 2000. View at Publisher · View at Google Scholar
  23. J. M. Smith, “Analyzing the mosaic structure of genes,” Journal of Molecular Evolution, vol. 34, no. 2, pp. 126–129, 1992. View at Google Scholar
  24. D. Posada, “Evaluation of methods for detecting recombination from DNA sequences: empirical data,” Molecular Biology and Evolution, vol. 19, no. 5, pp. 708–717, 2002. View at Google Scholar
  25. S. Sawyer, “Statistical tests for detecting gene conversion,” Molecular Biology and Evolution, vol. 6, no. 5, pp. 526–538, 1989. View at Google Scholar
  26. D. P. Martin, C. Williamson, and D. Posada, “RDP2: recombination detection and analysis from sequence alignments,” Bioinformatics, vol. 21, no. 2, pp. 260–262, 2005. View at Publisher · View at Google Scholar
  27. A. D. Tsaousis, D. P. Martin, E. D. Ladoukakis, D. Posada, and E. Zouros, “Widespread recombination in published animal mtDNA sequences,” Molecular Biology and Evolution, vol. 22, no. 4, pp. 925–933, 2005. View at Publisher · View at Google Scholar
  28. L. Wang, K. Zhang, and L. Zhang, “Perfect phylogenetic networks with recombination,” Journal of Computational Biology, vol. 8, no. 1, pp. 69–78, 2001. View at Publisher · View at Google Scholar
  29. T. C. Bruen, H. Philippe, and D. Bryant, “A simple and robust statistical test for detecting the presence of recombination,” Genetics, vol. 172, no. 4, pp. 2665–2681, 2006. View at Publisher · View at Google Scholar