Skip to main content
SpringerLink
Log in

Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology

  • Published:
Science in China Series C: Life Sciences Aims and scope Submit manuscript

Abstract

We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacteriologists’ taxonomy—primarily the latest online Outline of the Bergey’s Manual of Systematic Bacteriology. The CVTree phylogeny agrees very well with the Bergey’s taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Zuckerkandl E, Pauling L. Molecules as documents of evolutionary history. J Theor Biol, 1965, 8: 357–366

    Article  PubMed  CAS  Google Scholar 

  2. Driskell A C, Ané C, Burleigh J G, et al. Prospect for building the tree of life from large sequence databases. Science, 2004, 306: 1172–1174

    Article  PubMed  CAS  Google Scholar 

  3. Woese C R, Fox G E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA, 1977, 74: 5088–5090

    Article  PubMed  CAS  Google Scholar 

  4. Bergey’s Manual Trust. Bergey’s Manual of Systematic Bacteriology. 2nd ed, Vol 1–5. New York: Springer-Verlag. 2001–2008

    Google Scholar 

  5. Asai T, Zaporojets D, Squires C, et al. An Escherichia coli strain with all chromosomal rRNA operons inactivated: Complete exchange of rRNA genes between bacteria. Proc Natl Acad Sci USA, 1999, 96: 1971–1976

    Article  PubMed  CAS  Google Scholar 

  6. Teichmann S A, Mitchison G. Is there a phylogenetic signal in prokaryote proteins? J Mol Evol, 1999, 49: 98–107

    Article  PubMed  CAS  Google Scholar 

  7. Snel B, Huynen M A, Dutilh B E. Genome trees and the nature of genome evolution. Annu Rev Microbiol, 2005, 59: 191–209

    Article  PubMed  CAS  Google Scholar 

  8. Ciccarelli F D, Doerks T, von Mering C, et al. Toward automatic reconstruction of a highly resolved tree of life. Science, 2006, 311: 1283–1287

    Article  PubMed  CAS  Google Scholar 

  9. Qi J, Wang B, Hao B L. Whole genome prokaryote phylogeny without sequence alignment: A K-string composition approach. J Mol Evol, 2004, 58: 1–11

    Article  PubMed  CAS  Google Scholar 

  10. Hao B L, Qi J. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. J Bioinformatics & Computat Biol, 2004, 2: 1–19

    Article  CAS  Google Scholar 

  11. Qi J, Luo H, Hao B L. CVTree: A phylogenetic tree reconstruction tool based on whole genomes. Nucl Acids Res, 2004, 32, Web Server Issue: W45-W47

  12. A Supplementary Material to this paper is downloadable from either http://www.itp.ac.cn/hao/Suppl440.pdf or http://tlife.fudan.edu.cn/Suppl440.pdf

  13. Michel H. The future of the molecular biosciences: Consequences of the massive parallel approach. In: Lu Y X, eds. Sceince and Technology Development: A Retrospective View Over the Past Century and a Prospective Look Into the Future. Shanghai: Shanghai Education Press, 2000. 70

    Google Scholar 

  14. Shi X L, Xie H M, Zhang S Y, et al. Decomposition and reconstruction of protein sequences: The problem of uniqueness and factorizable language. J Korean Phys Soc, 2007, 50: 118–123

    Article  CAS  Google Scholar 

  15. Konstantinidis K T, Tiedje J M. Towards a genome-based taxonomy for prokaryotes. J Bacteriol, 2005, 187: 6258–6264

    Article  PubMed  CAS  Google Scholar 

  16. Garrity G M, Bell J A, Lilburn T G. Taxonomic Outline of the Prokayotes. Bergey’s Manual of Systematic Bacteriology. 2nd ed. New York: Spinger-Verlag, Rel 5.0, May 2004, doi: 10.1007/bergeysout-line200405

    Google Scholar 

  17. Margulis L, Schwartz K V. Five Kingdoms. An Illustrated Guide to the Phyla of Life on Earth. 3rd ed. New York: W H Freeman, 1998

    Google Scholar 

  18. Woese C R, Kandler O, Wheelis M L. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA, 1990, 87: 4576–4579

    Article  PubMed  CAS  Google Scholar 

  19. Nakabachi A, Yamashita A, Toh H, et al. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science, 2006, 314: 267

    Article  PubMed  CAS  Google Scholar 

  20. Johnson Z I, Zinser E R, Coe A, et al. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science, 2006, 311: 1737–1740

    Article  PubMed  CAS  Google Scholar 

  21. Coleman M C, Sullivan M B, Martiny A C, et al. Genome islands and the ecology and evolution of Prochlorococcus. Science, 2006, 311: 1768–1770

    Article  PubMed  CAS  Google Scholar 

  22. Woese C R, Olsen G J, Ibba M, et al. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol & Mol Biol Rev, 2000, 64: 202–236

    Article  CAS  Google Scholar 

  23. Pringshein E G. The relationship between bateria and Myxophyceae. Bacterial Rev, 1949, 13: 47

    Google Scholar 

  24. Zhi X Y, Cai M, Yang L L, et al. Evidence for the establishment of the Actinobacteria phylum. Microbiology (in Chinese), 2006, 33: 181–183

    Google Scholar 

  25. Garnier T, Eiglmeier K, Camus J C, et al. The complete genome of Mycobacterium bovis. Proc Natl Acad Sci USA, 2003, 100: 7877–7882

    Article  PubMed  CAS  Google Scholar 

  26. Murray R G E. The higher taxa, or, a place for everything ...? In: Bergey’s Manual of Systematic Bacteriology. 1st ed. Vol 4. Baltimore: Williams & Wilkins. 2329–2332

  27. Doolittle W F, Papke R T. Genomics and the bacterial species problem. Genome Res, 2006, 7: 116

    Google Scholar 

  28. Goffeau A. Life with 482 genes. Science, 1995, 270: 445–446

    Article  PubMed  CAS  Google Scholar 

  29. Burggraf S, Stetter K O, Pouviere P, et al. Methanopyrus kandleri: an archeal methanogen unrelated to all other known methanogens. Sys Appl Microbiol, 1991, 14: 346–381

    CAS  Google Scholar 

  30. Huynen M, Snel B, Bork P. Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes. Science, 1999, 286: 1443a

    Article  Google Scholar 

Download references

Author information

Author notes

  1. Qi Ji

    Present address: Center for Comparative Genomics and Bioinformatics, Penn State University, 310 Wartik Building, University Park, PA, 16802, USA

Authors and Affiliations

  1. Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, 100080, China

    Gao Lei, Qi Ji & Hao BaiLin

  2. T-Life Research Center, Fudan University, Shanghai, 200433, China

    Gao Lei, Sun JianDong & Hao BaiLin

  3. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, 101300, China

    Sun JianDong

  4. Santa Fe Institute, Santa Fe, NM87501, USA

    Hao BaiLin

Authors
  1. Gao Lei
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qi Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sun JianDong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hao BaiLin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hao BaiLin.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gao, L., Qi, J., Sun, J. et al. Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology. SCI CHINA SER C 50, 587–599 (2007). https://doi.org/10.1007/s11427-007-0084-3

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-007-0084-3

Keywords

Search

Navigation