This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Novichkov, P. S.
Right arrow Articles by Koonin, E. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Novichkov, P. S.
Right arrow Articles by Koonin, E. V.

 Previous Article  |  Next Article 

Journal of Bacteriology, January 2009, p. 65-73, Vol. 191, No. 1
0021-9193/09/$08.00+0     doi:10.1128/JB.01237-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes {triangledown}

Pavel S. Novichkov,1,{dagger} Yuri I. Wolf,1 Inna Dubchak,2,3 and Eugene V. Koonin1*

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894,1 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720,2 Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 945983

Received 4 September 2008/ Accepted 20 October 2008

In order to explore microevolutionary trends in bacteria and archaea, we constructed a data set of 41 alignable tight genome clusters (ATGCs). We show that the ratio of the medians of nonsynonymous to synonymous substitution rates (dN/dS) that is used as a measure of the purifying selection pressure on protein sequences is a stable characteristic of the ATGCs. In agreement with previous findings, parasitic bacteria, notwithstanding the sometimes dramatic genome shrinkage caused by gene loss, are typically subjected to relatively weak purifying selection, presumably owing to relatively small effective population sizes and frequent bottlenecks. However, no evidence of genome streamlining caused by strong selective pressure was found in any of the ATGCs. On the contrary, a significant positive correlation between the genome size, as well as gene size, and selective pressure was observed, although a variety of free-living prokaryotes with very close selective pressures span nearly the entire range of genome sizes. In addition, we examined the connections between the sequence evolution rate and other genomic features. Although gene order changes much faster than protein sequences during the evolution of prokaryotes, a strong positive correlation was observed between the "rearrangement distance" and the amino acid distance, suggesting that at least some of the events leading to genome rearrangement are subjected to the same type of selective constraints as the evolution of amino acid sequences.

* Corresponding author. Mailing address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894. Phone: (301) 435-5913. Fax: (301) 435-7794. E-mail: koonin{at}ncbi.nlm.nih.gov

{triangledown} Published ahead of print on 31 October 2008.

{dagger} Present address: Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720.

Journal of Bacteriology, January 2009, p. 65-73, Vol. 191, No. 1
0021-9193/09/$08.00+0     doi:10.1128/JB.01237-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Kuo, C.-H., Moran, N. A., Ochman, H. (2009). The consequences of genetic drift for bacterial genome complexity. Genome Res 19: 1450-1454 [Abstract] [Full Text]  
  • Kuo, C.-H., Ochman, H. (2009). Deletional Bias across the Three Domains of Life. Gen Biol Evol 2009: 145-152 [Abstract] [Full Text]  
  • Koonin, E. V. (2009). Darwinian evolution in the light of genomics. Nucleic Acids Res 37: 1011-1034 [Abstract] [Full Text]  
  • Zhulin, I. B. (2009). It Is Computation Time for Bacteriology!. J. Bacteriol. 191: 20-22 [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»