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

 Previous Article  |  Next Article 

Journal of Bacteriology, April 2002, p. 2260-2272, Vol. 184, No. 8
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.8.2260-2272.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Evolutionary Analysis by Whole-Genome Comparisons

Department of Computer Science, Kent State University, Kent, Ohio 44242,¹ Department of Biochemistry, University of Arizona, Tucson, Arizona 85721²

Received 20 August 2001/ Accepted 11 January 2002

A total of 37 complete genome sequences of bacteria, archaea, and eukaryotes were compared. The percentage of orthologous genes of each species contained within any of the other 36 genomes was established. In addition, the mean identity of the orthologs was calculated. Several conclusions result: (i) a greater absolute number of orthologs of a given species is found in larger species than in smaller ones; (ii) a greater percentage of the orthologous genes of smaller genomes is contained in other species than is the case for larger genomes, which corresponds to a larger proportion of essential genes; (iii) before species can be specifically related to one another in terms of gene content, it is first necessary to correct for the size of the genome; (iv) eukaryotes have a significantly smaller percentage of bacterial orthologs after correction for genome size, which is consistent with their placement in a separate domain; (v) the archaebacteria are specifically related to one another but are not significantly different in gene content from the bacteria as a whole; (vi) determination of the mean identity of all orthologs (involving hundreds of gene comparisons per genome pair) reduces the impact of errors in misidentification of orthologs and to misalignments, and thus it is far more reliable than single gene comparisons; (vii) however, there is a maximum amount of change in protein sequences of 37% mean identity, which limits the use of percentage sequence identity to the lower taxa, a result which should also be true for single gene comparisons of both proteins and rRNA; (viii) most of the species that appear to be specifically related based upon gene content also appear to be specifically related based upon the mean identity of orthologs; (ix) the genes of a majority of species considered in this study have diverged too much to allow the construction of all-encompassing evolutionary trees. However, we have shown that eight species of gram-negative bacteria, six species of gram-positive bacteria, and eight species of archaebacteria are specifically related in terms of gene content, mean identity of orthologs, or both.

This article has been cited by other articles:

• Yang, S., Doolittle, R. F., Bourne, P. E. (2005). Phylogeny determined by protein domain content. Proc. Natl. Acad. Sci. USA 102: 373-378 [Abstract] [Full Text]  
• Clarridge, J. E. III (2004). Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases. Clin. Microbiol. Rev. 17: 840-862 [Abstract] [Full Text]  
• Hao, W., Golding, G. B. (2004). Patterns of Bacterial Gene Movement. Mol Biol Evol 21: 1294-1307 [Abstract] [Full Text]  
• Coenye, T., Vandamme, P. (2003). Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiology 149: 3507-3517 [Abstract] [Full Text]  
• Bartolucci, S., Rossi, M., Cannio, R. (2003). Characterization and Functional Complementation of a Nonlethal Deletion in the Chromosome of a {beta}-Glycosidase Mutant of Sulfolobus solfataricus. J. Bacteriol. 185: 3948-3957 [Abstract] [Full Text]  
• Klotz, M. G., Loewen, P. C. (2003). The Molecular Evolution of Catalatic Hydroperoxidases: Evidence for Multiple Lateral Transfer of Genes Between Prokaryota and from Bacteria into Eukaryota. Mol Biol Evol 20: 1098-1112 [Abstract] [Full Text]  
• Jensen, L. J., Skovgaard, M., Brunak, S. (2002). Prediction of novel archaeal enzymes from sequence-derived features. Protein Sci. 11: 2894-2898 [Abstract] [Full Text]