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BioMed Research International
Volume 2013, Article ID 409062, 15 pages
http://dx.doi.org/10.1155/2013/409062
Research Article

Prokaryotic Phylogenies Inferred from Whole-Genome Sequence and Annotation Data

1Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
2College of Chemistry, Jilin University, Changchun 130012, China
3Department of Information and Communication Technology, University of Trento, 38050 Povo, Italy

Received 15 April 2013; Revised 26 June 2013; Accepted 22 July 2013

Academic Editor: Marco Bazzicalupo

Copyright © 2013 Wei Du 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. B. B. Ward, “How many species of prokaryotes are there?” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 16, pp. 10234–10236, 2002. View at Publisher · View at Google Scholar · View at Scopus
  2. C. R. Woese and G. E. Fox, “Phylogenetic structure of the prokaryotic domain: the primary kingdoms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 74, no. 11, pp. 5088–5090, 1977. View at Google Scholar · View at Scopus
  3. G. J. Olsen, C. R. Woese, and R. Overbeek, “The winds of (evolutionary) change: breathing new life into microbiology,” Journal of Bacteriology, vol. 176, no. 1, pp. 1–6, 1994. View at Google Scholar · View at Scopus
  4. M. A. Huynen and P. Bork, “Measuring genome evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 11, pp. 5849–5856, 1998. View at Publisher · View at Google Scholar · View at Scopus
  5. G. N. Lin, Z. Cai, G. Lin, S. Chakraborty, and D. Xu, “ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets,” BMC Bioinformatics, vol. 10, no. 1, article S5, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. G. J. Szollosi, B. Boussau, S. S. Abby, E. Tannier, and V. Daubin, “Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 43, pp. 17513–17518, 2012. View at Google Scholar
  7. W. F. Doolittle, “Phylogenetic classification and the universal tree,” Science, vol. 284, no. 5423, pp. 2124–2128, 1999. View at Publisher · View at Google Scholar · View at Scopus
  8. L. Hamel, N. Nahar, M. S. Poptsova, O. Zhaxybayeva, and J. P. Gogarten, “Unsupervised learning in detection of gene transfer,” Journal of Biomedicine and Biotechnology, vol. 2008, no. 1, Article ID 472719, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. 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 · View at Scopus
  10. A. Rokas, B. I. Williams, N. King, and S. B. Carroll, “Genome-scale approaches to resolving incongruence in molecular phylogenies,” Nature, vol. 425, no. 6960, pp. 798–804, 2003. View at Publisher · View at Google Scholar · View at Scopus
  11. S. Matsutani, “Links between repeated sequences,” Journal of Biomedicine and Biotechnology, vol. 2006, Article ID 13569, 3 pages, 2006. View at Publisher · View at Google Scholar · View at Scopus
  12. S. A. Teichmann and G. Mitchison, “Is there a phylogenetic signal in prokaryote proteins?” Journal of Molecular Evolution, vol. 49, no. 1, pp. 98–107, 1999. View at Publisher · View at Google Scholar · View at Scopus
  13. F. Ge, L.-S. Wang, and J. Kim, “The cobweb of life revealed by genome-scale estimates of horizontal gene transfer,” PLoS Biology, vol. 3, no. 10, article e316, 2005. View at Google Scholar · View at Scopus
  14. F. D. Ciccarelli, T. Doerks, C. Von Mering, C. J. Creevey, B. Snel, and P. Bork, “Toward automatic reconstruction of a highly resolved tree of life,” Science, vol. 311, no. 5765, pp. 1283–1287, 2006. View at Publisher · View at Google Scholar · View at Scopus
  15. V. Daubin, M. Gouy, and G. Perrière, “A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history,” Genome Research, vol. 12, no. 7, pp. 1080–1090, 2002. View at Publisher · View at Google Scholar · View at Scopus
  16. B. Snel, P. Bork, and M. A. Huynen, “Genome phylogeny based on gene content,” Nature Genetics, vol. 21, no. 1, pp. 108–110, 1999. View at Publisher · View at Google Scholar · View at Scopus
  17. S. R. Henz, D. H. Huson, A. F. Auch, K. Nieselt-Struwe, and S. C. Schuster, “Whole-genome prokaryotic phylogeny,” Bioinformatics, vol. 21, no. 10, pp. 2329–2335, 2005. View at Publisher · View at Google Scholar · View at Scopus
  18. Y. Luo, C. Fu, D.-Y. Zhang, and K. Lin, “BPhyOG: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes,” BMC Bioinformatics, vol. 8, article 266, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. E. J. Deeds, H. Hennessey, and E. I. Shakhnovich, “Prokaryotic phylogenies inferred from protein structural domains,” Genome Research, vol. 15, no. 3, pp. 393–402, 2005. View at Publisher · View at Google Scholar · View at Scopus
  20. X. Wu, Z. Cai, X.-F. Wan, T. Hoang, R. Goebel, and G. Lin, “Nucleotide composition string selection in HIV-1 subtyping using whole genomes,” Bioinformatics, vol. 23, no. 14, pp. 1744–1752, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Qi, H. Luo, and B. Hao, “CVTree: a phylogenetic tree reconstruction tool based on whole genomes,” Nucleic Acids Research, vol. 32, pp. W45–W47, 2004. View at Publisher · View at Google Scholar · View at Scopus
  22. J. Qi, B. Wang, and B.-I. Hao, “Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach,” Journal of Molecular Evolution, vol. 58, no. 1, pp. 1–11, 2004. View at Publisher · View at Google Scholar · View at Scopus
  23. Z. Xu and B. Hao, “CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes,” Nucleic Acids Research, vol. 37, no. 2, pp. W174–W178, 2009. View at Publisher · View at Google Scholar · View at Scopus
  24. L. Gao, J. Qi, J. Sun, and B. Hao, “Prokaryote phylogeny meets taxonomy: an exhaustive comparison of composition vector trees with systematic bacteriology,” Science in China, Series C, vol. 50, no. 5, pp. 587–599, 2007. View at Publisher · View at Google Scholar · View at Scopus
  25. X.-Y. Zhi, W. Zhao, W.-J. Li, and G.-P. Zhao, “Prokaryotic systematics in the genomics era,” Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, vol. 101, no. 1, pp. 21–34, 2012. View at Publisher · View at Google Scholar · View at Scopus
  26. J.-P. Doyon, V. Ranwez, V. Daubin, and V. Berry, “Models, algorithms and programs for phylogeny reconciliation,” Briefings in Bioinformatics, vol. 12, no. 5, Article ID bbr045, pp. 392–400, 2011. View at Publisher · View at Google Scholar · View at Scopus
  27. N. Saitou and M. Nei, “The neighbor-joining method: a new method for reconstructing phylogenetic trees,” Molecular Biology and Evolution, vol. 4, no. 4, pp. 406–425, 1987. View at Google Scholar · View at Scopus
  28. J. A. Studier and K. J. Keppler, “A note on the neighbor-joining algorithm of Saitou and Nei,” Molecular Biology and Evolution, vol. 5, no. 6, pp. 729–731, 1988. View at Google Scholar · View at Scopus
  29. G. M. Garrity, J. A. Bell, and T. G. Lilburn, Taxonomic Outline of the Procaryotes. Bergey's Manual of Systematic Bacteriology, Release 5.0, Springer, New York, NY, USA, 2nd edition, 2004.
  30. R. L. Tatusov, E. V. Koonin, and D. J. Lipman, “A genomic perspective on protein families,” Science, vol. 278, no. 5338, pp. 631–637, 1997. View at Publisher · View at Google Scholar · View at Scopus
  31. F. Mao, P. Dam, J. Chou, V. Olman, and Y. Xu, “DOOR: a database for prokaryotic operons,” Nucleic Acids Research, vol. 37, no. 1, pp. D459–D463, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. P. G. Vos, G. Jones, D. Krieg et al., Bergey's Manual of Systematic Bacteriology: Volume 3: The Firmicutes, Springer, New York, NY, USA, 2009.
  33. N. R. Krieg, W. Ludwig, W. Whitman et al., Bergey's Manual of Systematic Bacteriology: Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, Springer, New York, NY, USA, 2010.
  34. W. B. G. Whitman, P. Goodfellow, P. Kämpfer et al., Bergey's Manual of Systematic Bacteriology: Volume 5: The Actinobacteria, Springer, New York, NY, USA, 2012.
  35. V. Olman, H. Peng, Z. Su, and Y. Xu, “Mapping of microbial pathways through constrained mapping of orthologous genes,” in Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB '04), pp. 363–370, August 2004. View at Scopus
  36. F. Mao, Z. Su, V. Olman, P. Dam, Z. Liu, and Y. Xu, “Mapping of orthologous genes in the context of biological pathways: an application of integer programming,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 1, pp. 129–134, 2006. View at Publisher · View at Google Scholar · View at Scopus
  37. F. Zhou, V. Olman, and Y. Xu, “Barcodes for genomes and applications,” BMC Bioinformatics, vol. 9, article 546, 2008. View at Publisher · View at Google Scholar · View at Scopus
  38. G. Wang, F. Zhou, V. Olman, F. Li, and Y. Xu, “Prediction of pathogenicity islands in Enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes,” FEBS Letters, vol. 584, no. 1, pp. 194–198, 2010. View at Publisher · View at Google Scholar · View at Scopus
  39. A. Kanhere and M. Vingron, “Horizontal gene transfers in prokaryotes show differential preferences for metabolic and translational genes,” BMC Evolutionary Biology, vol. 9, no. 1, article 9, 2009. View at Publisher · View at Google Scholar · View at Scopus
  40. F. Pukelsheim, “The three sigma rule,” The American Statistician, vol. 48, pp. 88–91, 1994. View at Google Scholar
  41. E. V. Koonin, K. S. Makarova, and L. Aravind, “Horizontal gene transfer in prokaryotes: quantification and classification,” Annual Review of Microbiology, vol. 55, pp. 709–742, 2001. View at Publisher · View at Google Scholar · View at Scopus
  42. Q. Li, Z. Xu, and B. Hao Bailin, “Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations,” Journal of Biotechnology, vol. 149, no. 3, pp. 115–119, 2010. View at Publisher · View at Google Scholar · View at Scopus
  43. G. M. Garrity, K. L. Johnson, J. A. Bell, and D. B. Searles, Taxonomic Outline of the Procaryotes, Bergey's Manual of Systematic Bacteriology, Release 3.0, Springer, New York, NY, USA, 2nd edition, 2002.
  44. G. M. Garrity, T. G. Lilburn, J. R. Cole, S. H. Harrison, J. Euzéby, and B. J. Tindall, The Taxonomic Outline of Bacteria and Archaea (TOBA), Release 7.7, Michigan State University Board of Trustees, East Lansing, Mitch, USA, 2007.