Computational inference of scenarios for α-proteobacterial genome evolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 101, Issue 26, 2004, Pages 9722-9727

  Boussau, Bastien ^a   Karlberg, E Olof ^a   Frank, A Carolin ^a   Legault, Boris Antoine ^a   Andersson, Siv G E ^a,b  

^a UPPSALA UNIVERSITY   (Sweden)

^b Department of Molecular Evolution ^*  (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; GENOME SIZE; GRAM NEGATIVE BACTERIUM; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL;

ALPHAPROTEOBACTERIA; ANIMALS; CHROMOSOMES, BACTERIAL; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENOME, BACTERIAL; HUMANS; MITOCHONDRIA; PHYLOGENY; PLANTS;

ALPHAPROTEOBACTERIA; ANIMALIA; BACTERIA (MICROORGANISMS); EUKARYOTA; NEGIBACTERIA; PROKARYOTA; PROTEOBACTERIA;

EID: 3042840997     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0400975101     Document Type: Article

References (32)

1. Doolittle, W. F. (1999) Science 284, 2124-2128.
2. Snel, B., Bork, P. & Huynen, M. (1999) Nat. Genet. 21, 108-110.
3. Sicheritz-Ponten, T. & Andersson, S. G. E. (2001) Nucleic Acids Res. 29, 545-552.
4. Kurland, C. G., Canback, B. & Berg, O. G. (2003) Proc. Natl. Acad. Sci. USA 100, 9658-9662.
5. Daubin, V., Moran, N. A. & Ochman, H. (2003) Science 301, 829-832.
6. Andersson, S. G. E., Zomorodipour, A., Andersson, J. O., Sicheritz-Ponten, T., Alsmark, U. C. M., Podowski, R. M., Näslund, K., Eriksson, A.-S., Winkler, H. H. & Kurland, C. G. (1998) Nature 396, 133-140.
7. Ogata, H., Audic, S., Renesto-Audiffren, P., Fournier, P. E., Barbe, V., Samson, D., Roux, V., Cossart, P., Weissenbach, J., Claverie, J. M. & Raoult, D. (2001) Science 293, 2093-2098.
8. Goodner, B., Hinkle, G., Gattung, S., Miller, N., Blanchard, M., Qurollo, B., Goldman, B. S., Cao, Y., Askenazi, M., Halling, C., et al. (2001) Science 294, 2323-2328.
9. Wood, D. W., Setubal, J. C., Kaul, R., Monks, D. E., Kitajima, J. P., Okura, V. K., Zhou, Y., Chen, L., Wood, G. E., Almeida, N. F., Jr., et al. (2001) Science 294, 2317-2322.
10. Galibert, F., Finan, T. M., Long, S. R., Puhler, A., Abola, P., Ampe, F., Barloy-Hubler, F., Barnett, M. J., Becker, A., Boistard, P., et al. (2001) Science 293, 668-672.
11. Kaneko, T., Nakamura, Y., Sato, S., Minamisawa, K., Uchiumi, T., Sasamoto, S., Watanabe, A., Idesawa, K., Iriguchi, M., Kawashima, K., et al. (2002) DNA Res. 9, 189-197.
12. Wu, M., Sun, L. V., Vamathevan, J., Riegler, M., Deboy, R., Brownlie, J. C., McGraw, E. A., Martin, W., Esser, C., Ahmadinejad, N., et al. (2004) PLoS Biol. 2, 327-341.
13. Gray, M., Burger, G. & Lang, B. F. (1999) Science 283, 1476-1481.
14. Karlberg, O. & Andersson, S. G. E. (2003) Nat. Rev. Genet. 4, 391-397.
15. Gabaldon, T. & Huynen, M. A. (2003) Science 301, 609.
16. Karlberg, E. O., Canbäck, B., Kurland, C. G. & Andersson, S. G. E. (2000) Yeast 17, 170-187.
17. Tamas, I., Klasson, L., Canbäck, B., Näslund, A. K., Eriksson, A.-S., Wernegreen, J. J., Sandström, J. P., Moran, N. A. & Andersson, S. G. E. (2002) Science 296, 2376-2379.
18. Snel, B., Bork, P. & Huynen, M. (2002) Genome Res. 12, 17-25.
19. Mirkin, B. G., Fenner, T. I., Galperin, M. Y. & Koonin, E. V. (2003) BMC Evol. Biol. 3, 2.
20. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Liplman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
21. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680.
22. Guindon, S. & Gascuel, O. (2003) Syst. Biol. 52, 696-704.
23. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. (1997) Science 278, 631-637.
24. Swofford, D. L. (1998) Phylogenetic Analysis Using Parsimony (PAUP) (Sinauer, Sunderland, MA), Version 4.0b10.
25. Nimwegen, E. (2003) Trends Genet. 19, 479-484.
26. Konstantinidis, K. T. & Tiedje, J. M. (2004) Proc. Natl. Acad. Sci. USA 101, 3160-3165.
27. Klasson, L. & Andersson, S. G. E. (2004) Trends Microbiol. 12, 37-43.
28. Koonin, E. V. (2000) Annu. Rev. Genomics Hum. Genet. 1, 99-116.
29. Kobayashi, K. (2003) Proc. Natl. Acad. Sci. USA 100, 4678-4683.
30. Olsen, G. J., Woese, C. R. & Overbeek, R. (1994) J. Bacteriol. 176, 1-6.
31. Viale, A. & Arakaki, A. K. (1994) FEBS Lett. 341, 146-151.
32. Emelyanov, V. (2003) Arch. Biochem. Biophys. 420, 130-141.