[1]
|
Stackebrandt, E., Murray, R.G.E. and Trüper, H.G. (1988) Proteobacteria classis nov., a name for the phylogenetic taxon that includes the “purple bacteria and their relatives”. International Journal of Systematic Bacteriology, 38, 321-325.
|
[2]
|
Gupta, R.S. (2000) The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiology Reviews, 24, 367-402.
|
[3]
|
Fox, G.E., Stackebrandt, E., Hespell R.B., Gibson J., Maniloff, J., Dyer, T.A., Wolfe, R.S., Balch, W.E., Tanner, R.S., Magrum, L.J., Zablen, L.B., Blakemore, R., Gupta, R., Bonen, L., Lewis, B.J., Stahl, D.A., Luehrsen, K. R., Chen, K.N. and Woese, C.R. (1980) The phylogeny of prokaryotes. Science, 209, 457-463.
|
[4]
|
Woese, C.R., Stackebrandt, E., Macke, T.J. and Fox, G. E. (1985a) A phylogenetic definition of the major eubacterial taxa. Systematic and Applied Microbiology, 6, 143151.
|
[5]
|
Woese, C.R. (1987) Bacterial Evolution. FEMS Microbiology Reviews, 51, 221-271.
|
[6]
|
De Ley, J. (1992) The proteobacteria: Ribosomal RNA cistron similarities and bacterial taxonomy. In: by Balows, A., Trüper, H.G., Dworkin, M., Harder, W., and Schleifer, K.H., Eds., The Prokaryotes, 2nd Edition, Springer-Verlag, Berlin, pp. 2111-2140.
|
[7]
|
Woese, C.R., Stackebrandt, E., Weisburg, W.G., Paster, B. J., Madigan, M.T., Fowler, V.J., Hahn, C.M., Blanz, P., Gupta, R., Nealson, K.H. and Fox, G.E. (1984a) The phylogeny of purple bacteria: the alpha subdivision. Systematic and Applied Microbiology, 5, 315-326.
|
[8]
|
Woese, C.R., Weisburg, W.G., Paster, B.J., Hahn, C.M., Tanner, R.S., Krieg, N.R., Koops, H.-P., Harms, H. and Stackebrandt, E. (1984b) The phylogeny of purple bacteria: the beta subdivision. Systematic and Applied Microbiology, 5, 327-336.
|
[9]
|
Woese, C.R., Weisburg, W.G., Hahn, C.M., Paster, B.J., Zablen, L.B., Lewis, B.J., Macke, T.J., Ludwig, W. and Stackebrandt, E. (1985b) The phylogeny of purple bacteria: the gamma subdivision. Systematic and Applied Microbiology, 6, 25-33.
|
[10]
|
Brenner D.J., Krieg N.R., Staley J.T. and Garrity G.M., (Eds.) (2005) Bergey’s Manual of Systematic Bacteriology, 2nd Edition, Vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), Springer, New York.
|
[11]
|
Kersters, K., Devos, P., Gillis, M., Swings, J., Vandamme, P. and Stackebrandt, E. (2006) Introduction to the Proteobacteria. In Dworkin, M., Falkow, S., Rosenberg, E. Schleifer, K.H. and Stackebrandt, E. (Eds.), The Prokaryotes: A Handbook on the Biology of Bacteria. Springer, New York, pp. 3-37.
|
[12]
|
Belda, E., Moya, A. and Silva, F.J. (2005) Genome rearrangement distances and gene order phylogeny in γ-proteobacteria. Molecular Biology and Evolution, 22, 14561467.
|
[13]
|
Woese, C.R., Kandler, O. and Wheelis, M.L. (1990) Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eucarya. Proceedings of the National Academy of Sciences, USA, 87, 4576-4579.
|
[14]
|
Ludwig, W. and Klenk, H.P. (2005) Overview: A phylogenetic backbone and taxonomic framework for prokaryotic systematics. In: Brenner, D.J. Krieg, N.R. Staley J.T. and Garrity, G.M. (Eds.), Bergey’s Manual of Systematic Bacteriology, Springer-Verlag, Berlin, pp. 49-65.
|
[15]
|
Anton, A.I., Martinez-Murcia, A.J. and Rodriguez-Valera, F. (1998) Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. Journal of Molecular Evolution, 47(1), 62-72.
|
[16]
|
Giannino, V., Rappazzo, G., Scuto, A., Di Marco, O., Privitera, A., Santagati, M. and Stefani S. (2001) rrn operons in Haemophilus parainfluenzae and mosaicism of conserved and species-specific sequences in the 16S-23S rDNA long spacer. Research in Microbiology, 152(5), 461-468.
|
[17]
|
Goncalves, E.R. and Rosato, Y.B. (2002) Phylogenetic analysis of Xanthomonas species based upon 16S--23S rDNA intergenic spacer sequences. International Journal of Systematic and Evolutionary Microbiology, 52, 355-361.
|
[18]
|
Wang, M., Cao, B., Yu, Q., Liu, L., Gao, Q., Wang, L. and Feng, L. (2008) Analysis of the 16S-23S rRNA gene internal transcribed spacer region in Klebsiella species. Journal of Clinical Microbiology, 46, 3555-3563.
|
[19]
|
Tambong, J.T., Xu, R. and Bromfield, E.S.P. (2009) Intercistronic heterogeneity of the 16S-23S rRNA spacer region among Pseudomonas strains isolated from subterranean seeds of hog peanut (Amphicarpa bracteata). Microbiology, 155, 2630-2640.
|
[20]
|
Kunisawa, T. (2001) Gene arrangements and phylogeny in the class Proteobacteria. Journal of Theoretical Bio logy, 213, 9-19.
|
[21]
|
Lerat, E., Daubin, V. and Moran, N.A. (2003) From gene trees to organismal phylogeny in prokaryotes: The case of the γ-proteobacteria. Public Library of Science Biology, 1, e19.
|
[22]
|
Brown, J.R. and Volker, C. (2004) Phylogeny of γ –proteobacteria: Resolution of one branch of the universal tree? Bioessays, 26, 463-468.
|
[23]
|
Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B. and Bork, P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science, 311, 1283-1287.
|
[24]
|
Mrazek, J., Spormann, A.M. and Karlin, S. (2006) Genomic comparisons among γ-proteobacteria. Environmental Microbiology, 8, 273-288.
|
[25]
|
Lee, H.Y. and Côté, J.-C. (2006) Phylogenetic analysis of γ-proteobacteria inferred from nucleotide sequence comparisons of the house-keeping genes adk, aroE and gdh: comparisons with phylogeny inferred from 16S rRNA gene sequences. Journal of General and Applied Microbiology, 52, 147-158.
|
[26]
|
Gao, B., Mohan, R. and Gupta, R.S. (2009) Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. International Journal of Systematic and Evolutionary Microbiology, 59, 234-247.
|
[27]
|
Xu, D. and Côté, J.-C. (2003) Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3’ end 16S rDNA and 5’ end 16S23S ITS nucleotide sequences. International Journal of Systematic and Evolutionary Microbiology, 53, 695-704.
|
[28]
|
Yakoubou, S., Xu, D. and Côté, J.-C. Phylogeny of Bacillales inferred from 3’ 16S rDNA and 5’ 16S-23S ITS nucleotide sequences. Nature Science, in Press.
|
[29]
|
Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680.
|
[30]
|
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
|
[31]
|
Kimura, M. (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
|
[32]
|
Page, R.D.M. (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Application in the Biosciences, 12, 357-358.
|
[33]
|
Page, R.D.M. (2000) TreeView—tree drawing software for Apple Macintosh and Windows. http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
|
[34]
|
Gürtler, V. and Stanisich V. A. (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology, 142, 3-16.
|
[35]
|
Suen G., Goldman, B. S. and Welch, R. D. (2007) Predicting Prokaryotic Ecological Niches Using Genome Sequence Analysis. Public Library of Science Biology ONE, 2(8), e743.
|
[36]
|
Ivanova, E. P., Flavier, S. and Christen, R. (2004) Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromona-daceae fam. nov. International Journal of Systematic and Evolutionary Microbiology, 54, 1773-1788.
|