Extracting phylogenetic information from whole-genome sequencing projects: The lactic acid bacteria as a test case

Microbiology

Volumn 149, Issue 12, 2003, Pages 3507-3517

  Coenye, Tom ^a   Vandamme, Peter ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; RNA 16S;

ARTICLE; BACTERIAL GENOME; CODON; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE ORDER; GENE TRANSFER; GENETIC CODE; GENETIC CONSERVATION; LACTIC ACID BACTERIUM; MICROBIOLOGICAL PARAMETERS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; TAXONOMY;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0346882654     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.26515-0     Document Type: Article

References (68)

1. Ahmad, S., Selvapandiyan, A. & Bhatnagar, R. K. (2000). Phylogenetic analysis of gram-positive bacteria based on grpE, encoded by the dnaK operon. Int J Syst Evol Microbiol 50, 1761-1766.
2. Ajdic, D., McShan, W. M., McLaughlin, R. E. & 16 other authors (2002). Genome sequence of Streptococcus mutans UA159, a cario-genic dental pathogen. Proc Natl Acad Sci U S A 99, 14434-14439.
3. 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.
4. Andersson, S. G. E. & Sharp, P. M. (1996). Codon usage in the Mycobacterium tuberculosis complex. Microbiology 142, 915-925.
5. Bansal, A. K. & Meyer, T. E. (2002). Evolutionary analysis by whole-genome comparisons. J Bacteriol 184, 2260-2272.
6. Bentley, R. W., Leigh, J. A. & Collins, M. D. (1991). Intrageneric structure of Streptococcus based on comparative analysis of small-subunit rRNA sequences. Int J Syst Bacteriol 41, 487-494.
7. Beres, S. B., Sylva, G. L., Barbian, K. D. & 13 other authors (2002). Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc Natl Acad Sci U S A 99, 10078-10083.
8. Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., Ehrlich, S. D. & Sorokin, A. (2001). The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 11, 731-753.
9. Brocchieri, L. (2001). Phylogenetic inferences from molecular sequences: review and critique. Theor Pop Biol 59, 27-40.
10. 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.
11. 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.
12. Daubin, V., Gouy, M. & Perriere, G. (2001). Bacterial molecular phylogeny using supertree approach. Genome Inform 12, 155-164.
13. Diaz-Lazcoz, Y., Aude, J. C., Nitschke, P., Chiapello, H., Landes-Devauchelle, C. & Risler, J. L. (1998). Evolution of genes, evolution of species: the case of aminoacyl-tRNA synthetases. Mol Biol Evol 15, 1548-1561.
14. Eisen, J. A. (1995). The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 41, 1105-1123.
15. Eisen, J. A. (2000). Assessing evolutionary relationships among microbes from whole-genome analysis. Curr Opin Microbiol 3, 475-480.
16. Enright, M. C. & Spratt, B. G. (1999). Extensive variation in the ddl gene of penicillin-resistant Streptococcus pneumoniae results from a hitchhiking effect driven by the penicillin-binding protein 2b gene. Mol Biol Evol 16, 1687-1695.
17. Felsenstein, J. (1988). Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22, 521-565.
18. Felsenstein, J. (1996). Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 266, 418-427.
19. Feng, D. F., Cho, G. & Doolittle, R. F. (1997). Determining divergence times with a protein clock: update and reevaluation. Proc Natl Acad Sci U S A 94, 13028-13033.
20. Ferretti, J. J., McShan, W. M., Ajdic, D. & 20 other authors (2001). Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A 98, 4658-4663.
21. Fitz-Gibbon, S. & House, C. H. (1999). Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27, 4218-4222.
22. Fleischmann, R. D., Adams, M. D., White, O. & 37 other authors (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512.
23. Forterre, P. & Philippe, H. (1999). Where is the root of the universal tree of life? Bioessays 21, 871-879.
24. Garrity, G. M. & Holt, J. G. (2001). The road map to the manual. In Bergey's Manual of Systematic Bacteriology, Vol. 1, 2nd edn, pp. 119-141. Edited by D. R. Boone & R. W. Castenholz. New York: Springer.
25. Glaser, P., Rusniok, C., Buchrieser, C. & 9 other authors (2002). Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Mol Microbiol 45, 1499-1513.
26. 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.
27. Gupta, R. S. & Griffiths, E. (2002). Critical issues in bacterial phylogeny. Theor Popul Biol 61, 423-434.
28. Hoskins, J., Alborn, W. E., Arnold, J. & 39 other authors (2001). Genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol 183, 5709-5717.
29. House, C. H. & Fitz-Gibbon, S. T. (2002). Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54, 539-547.
30. Huang, W. M. (1996). Bacterial diversity based on type II DNA topoisomerase genes. Annu Rev Genet 30, 79-107.
31. Huynen, M. A. & Bork, P. (1998). Measuring genome evolution. Proc Natl Acad Sci U S A 95, 5849-5856.
32. Karlin, S., Mrazek, J. & Campbell, A. M. (1997). Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179, 3899-3913.
33. Karlin, S., Campbell, A. M. & Mrazek, J. (1998). Comparative DNA analysis across diverse genomes. Annu Rev Genet 32, 185-225.
34. Kawamura, Y., Hou, X. G., Sultana, E., Miura, H. & Ezaki, T. (1995). Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Int J Syst Bacteriol 45, 406-408.
35. Klaenhammer, T., Altermann, E., Arigoni, F. & 33 other authors (2002). Discovering lactic acid bacteria by genomics. Antonie Van Leeuwenhoek 82, 29-58.
36. Kleerebezem, M., Boekhorst, J., van Kranenburg, R. & 17 other authors (2003). Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A 100, 1990-1995.
37. Kolsto, A. B. (1997). Dynamic bacterial genome organization. Mol Microbiol 24, 241-248.
38. Kunisawa, T. (2001). Gene arrangements and phylogeny in the class Proteobacteria. J Theor Biol 213, 9-19.
39. Lan, R. & Reeves, P. R. (1996). Gene transfer is a major factor in bacterial evolution. Mol Biol Evol 13, 47-55.
40. Lin, J. & Gerstein, M. (2000). Whole-genome trees based on the Occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 10, 808-818.
41. Nölling, J., Breton, G., Omelchenko, M. V. & 16 other authors (2001). Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 183, 4823-4838.
42. Ochman, H., Lawrence, J. G. & Groisman, E. A. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304.
43. Okstad, O. A., Hegna, I., Lindback, T., Rishovd, A. L. & Kolsto, A. B. (1999). Genome organization is not conserved between Bacillus cereus and Bacillus subtilis. Microbiology 145, 621-631.
44. Pot, B., Ludwig, W., Kersters, K. & Schleifer, K. H. (1994). Taxonomy of lactic acid bacteria. In Bacteriocins of the Lactic Acid Bacteria: Microbiology, Genetics and Applications. Edited by L. De Vuyst & E. J. Vandamme. London: Chapman & Hall.
45. Poyart, C., Quesne, G., Coulon, S., Berche, P. & Trieu-Cuot, P. (1998). Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J Clin Microbiol 36, 41-47.
46. Rossello-Mora, R. & Amann, R. (2001). The species concept for prokaryotes. FEMS Microbiol Rev 25, 39-67.
47. Roux, V., Rydkina, E., Eremeeva, M. & Raoult, D. (1997). Citrate synthase gene comparison, a new tool for phylogenetic analysis, and its application for the Rickettsiae. Int J Syst Bacteriol 47, 252-261.
48. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M. A. & Barell, B. G. (2000). Artemis: sequence visualisation and annotation. Bioinformatics 16, 944-945.
49. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
50. Schell, M. A., Karmirantzou, M., Snel, B. & 9 other authors (2002). The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A 99, 14422-14427.
51. Smoot, J. C., Barbian, K. D., Van Gompel, J. J. & 15 other authors (2002). Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc Natl Acad Sci U S A 99, 4668-4673.
52. Snel, B., Bork, P. & Huynen, M. A. (1999). Genome phylogeny based on gene content. Nat Genet 21, 108-110.
53. Snel, B., Bork, P. & Huynen, M. A. (2002). Genomes in flux: the evolution of archeal and proteobacterial gene content. Genome Res 12, 17-25.
54. Stackebrandt, E., Frederiksen, W., Garrity, G. M. & 10 other authors (2002). Report of the ad-hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
55. Suyama, M. & Bork, P. (2001). Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet 17, 10-13.
56. Swofford, D. L. & Olsen, G. J. (1990). Phylogeny reconstruction. In Molecular Systematics. Edited by D. M. Hillis & C. Moritz. Sunderland, MA: Sinauer Associates.
57. Tamames, J., Casari, G., Ouzounis, C. & Valencia, A. (1997). Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol 44, 66-73.
58. Teichmann, S. A. & Mitchison, G. (1999). Is there a phylogenetic signal in prokaryote proteins? J Mol Evol 49, 98-107.
59. Tekaia, F., Lazcano, A. & Dujon, B. (1999). The genomic tree as revealed from whole proteome comparisons. Genome Res 9, 550-557.
60. Tekaia, F., Yeramian, E. & Dujon, B. (2002). Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene 297, 51-60.
61. Tettelin, H., Nelson, K. E., Paulsen, I. T. & 36 other authors (2001). Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293, 498-506.
62. Tettelin, H., Masignani, V., Cieslewicz, M. J. & 40 other authors (2002). Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A 99, 12391-12396.
63. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J. (1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407-438.
64. Wheelis, M. L., Kandler, O. & Woese, C. R. (1992). On the nature of global classification. Proc Natl Acad Sci U S A 89, 2930-2934.
65. 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.
66. Wolf, Y. I., Rogozin, I. B., Grishin, N. V. & Koonin, E. V. (2002). Genome trees and the tree of life. Trends Genet 18, 472-479.
67. Wright, F. (1990). The 'effective number of codons' used in a gene. Gene 87, 23-29.
68. Zeigler, D. R. (2003). Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53, 1893-1900.