1887

Abstract

The phylogenetic placement of was investigated on the basis of gene order data from completely sequenced bacterial genomes. was found to share four gene arrangements characteristic of the , , , , , , , and termite group 1, the presence of which defines superphylum 2. The remaining phyla show sets of alternative gene arrangements and form superphylum 1. An analysis of conserved gene pairs showed that the overall genome organization of is most similar to that of deltaproteobacteria. Three arrangements that suggest gene translocations were identified that are likely to have occurred in a common ancestor of and the exclusive of virtually all other major bacterial phyla. The translocation events suggest the closest evolutionary relationship between and the .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.014266-0
2010-05-01
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/5/1090.html?itemId=/content/journal/ijsem/10.1099/ijs.0.014266-0&mimeType=html&fmt=ahah

References

  1. Achenbach-Richter, L., Gupta, R., Stetter, K. O. & Woese, C. R. ( 1987; ). Were the original eubacteria thermophiles? Syst Appl Microbiol 9, 34–39.[CrossRef]
    [Google Scholar]
  2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  3. Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E. & Stanhope, M. J. ( 2001; ). Universal trees based on large combined protein sequence data sets. Nat Genet 28, 281–285.[CrossRef]
    [Google Scholar]
  4. Castro, H. F., Williams, N. H. & Ogram, A. ( 2000; ). Phylogeny of sulfate-reducing bacteria. FEMS Microbiol Ecol 31, 1–9.
    [Google Scholar]
  5. Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B. & Bork, P. ( 2006; ). Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283–1287.[CrossRef]
    [Google Scholar]
  6. Coenye, T. & Vandamme, P. ( 2004; ). A genomic perspective on the relationship between the Aquificales and the epsilon-Proteobacteria. Syst Appl Microbiol 27, 313–322.[CrossRef]
    [Google Scholar]
  7. Dandekar, T., Snel, B., Huynen, M. & Bork, P. ( 1998; ). Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23, 324–328.[CrossRef]
    [Google Scholar]
  8. Daubin, V., Gouy, M. & Perriere, G. ( 2002; ). A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12, 1080–1090.[CrossRef]
    [Google Scholar]
  9. Delsuc, F., Brinkmann, H. & Philippe, H. ( 2005; ). Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6, 361–375.
    [Google Scholar]
  10. Etchebehere, C., Pavan, M. E., Zorzópulos, J., Soubes, M. & Muxí, L. ( 1998; ). Coprothermobacter platensis sp. nov., a new anaerobic proteolytic thermophilic bacterium isolated from an anaerobic mesophilic sludge. Int J Syst Bacteriol 48, 1297–1304.[CrossRef]
    [Google Scholar]
  11. Griffiths, E. & Gupta, R. S. ( 2004; ). Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. Int Microbiol 7, 41–52.
    [Google Scholar]
  12. Griffiths, E. & Gupta, R. S. ( 2007; ). Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae. Microbiology 153, 2648–2654.[CrossRef]
    [Google Scholar]
  13. Gupta, R. S. ( 1998; ). Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol Mol Biol Rev 62, 1435–1491.
    [Google Scholar]
  14. Gupta, R. S. ( 2003; ). Evolutionary relationships among photosynthetic bacteria. Photosynth Res 76, 173–183.[CrossRef]
    [Google Scholar]
  15. Gupta, R. S. & Griffiths, E. ( 2002; ). Critical issues in bacterial phylogenies. Theor Popul Biol 61, 423–434.[CrossRef]
    [Google Scholar]
  16. Henry, E. A., Devereux, R., Maki, J. S., Gilmour, C. C., Woese, C. R., Mandelco, L., Schauder, R., Remsen, C. C. & Mitchell, R. ( 1994; ). Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch Microbiol 161, 62–69.[CrossRef]
    [Google Scholar]
  17. Hugenholtz, P., Goebel, B. M. & Pace, N. R. ( 1998; ). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180, 4765–4774.
    [Google Scholar]
  18. Iyer, L. M., Koonin, E. V. & Aravind, L. ( 2004; ). Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335, 73–88.[CrossRef]
    [Google Scholar]
  19. Jain, R., Rivera, M. C. & Lake, J. A. ( 1999; ). Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A 96, 3801–3806.[CrossRef]
    [Google Scholar]
  20. Korbel, J. O., Snel, B., Huynen, M. A. & Bork, P. ( 2002; ). shot: a web server for the construction of genome phylogenies. Trends Genet 18, 158–162.[CrossRef]
    [Google Scholar]
  21. Koski, L. B. & Golding, G. B. ( 2001; ). The closest blast hit is often not the nearest neighbor. J Mol Evol 52, 540–542.[CrossRef]
    [Google Scholar]
  22. Kunisawa, T. ( 2001; ). Gene arrangements and phylogeny in the class Proteobacteria. J Theor Biol 213, 9–19.[CrossRef]
    [Google Scholar]
  23. Kunisawa, T. ( 2003; ). Gene arrangements and branching orders of Gram-positive bacteria. J Theor Biol 222, 495–503.[CrossRef]
    [Google Scholar]
  24. Kunisawa, T. ( 2006; ). Dichotomy of major bacterial phyla inferred from gene arrangement comparisons. J Theor Biol 239, 367–375.[CrossRef]
    [Google Scholar]
  25. Lowe, T. M. & Eddy, S. R. ( 1997; ). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25, 955–964.[CrossRef]
    [Google Scholar]
  26. Pearson, W. R. & Lipman, D. J. ( 1988; ). Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85, 2444–2448.[CrossRef]
    [Google Scholar]
  27. Saiki, T., Kobayashi, Y., Kawagoe, K. & Beppu, T. ( 1985; ). Dictyoglomus thermophilum gen. nov., sp. nov., a chemoorganotrophic, anaerobic, thermophilic bacterium. Int J Syst Bacteriol 35, 253–259.[CrossRef]
    [Google Scholar]
  28. Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B. F. & Cedergren, R. ( 1992; ). Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc Natl Acad Sci U S A 89, 6575–6579.[CrossRef]
    [Google Scholar]
  29. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. ( 1997; ). A genomic perspective on protein families. Science 278, 631–637.[CrossRef]
    [Google Scholar]
  30. Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., Rao, B. S., Kiryutin, B., Galperin, M. Y., Fedorova, N. D. & Koonin, E. V. ( 2001; ). The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29, 22–28.[CrossRef]
    [Google Scholar]
  31. Teeling, H., Lombardot, T., Bauer, M., Ludwig, W. & Glöckner, F. O. ( 2004; ). Evaluation of the phylogenetic position of the planctomycete ‘Rhodopirellula baltica’ SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. Int J Syst Evol Microbiol 54, 791–801.[CrossRef]
    [Google Scholar]
  32. Teske, A., Alm, E., Regan, J. M., Toze, S., Rittmann, B. E. & Stahl, D. A. ( 1994; ). Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J Bacteriol 176, 6623–6630.
    [Google Scholar]
  33. Wagner, M. & Horn, M. ( 2006; ). The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17, 241–249.[CrossRef]
    [Google Scholar]
  34. Ward, N. L., Challacombe, J. F., Janssen, P. H., Henrissat, B., Coutinho, P. M., Wu, M., Xie, G., Haft, D. H., Sait, M. & other authors ( 2009; ). Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils. Appl Environ Microbiol 75, 2046–2056.[CrossRef]
    [Google Scholar]
  35. Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Tatusov, R. L. & Koonin, E. V. ( 2001; ). Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1, 8 [CrossRef]
    [Google Scholar]
  36. Wu, M. & Eisen, J. A. ( 2008; ). A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9, R151 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.014266-0
Loading
/content/journal/ijsem/10.1099/ijs.0.014266-0
Loading

Data & Media loading...

Supplements

vol. , part 5, pp. 1090 - 1102

Completely sequenced genomes used in this analysis.

BLAST best-hit analyses of ribosomal proteins from as query.

[PDF file of Supplementary Tables](131 KB)



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error