The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Measuring genome evolution
Open accessAbstract
The determination of complete genome sequences provides us with an opportunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to their protein coding genes at two levels: ( i ) we compare genomes as “bags of genes” and measure the fraction of orthologs shared between genomes and ( ii ) we quantify correlations between genes with respect to their relative positions in genomes. Distances between the genomes are related to their divergence times, measured as the number of amino acid substitutions per site in a set of 34 orthologous genes that are shared among all the genomes compared. We establish a hierarchy of rates at which genomes have changed during evolution. Protein sequence identity is the most conserved, followed by the complement of genes within the genome. Next is the degree of conservation of the order of genes, whereas gene regulation appears to evolve at the highest rate. Finally, we show that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes.
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Cites
The genetical theory of natural selection
Fisher, R. A. (1930) · doi:10.5962/bhl.title.27468 · Cited by 17,617
The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessières, P., Bolotin, A., Borchert, S., et al. (1997) · Nature · doi:10.1038/36786 · Cited by 3,679
The complete genome sequence of the gastric pathogen Helicobacter pylori
Tomb, J.-F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., Ketchum, K. A., Klenk, H. P., Gill, S., Dougherty, B. A., et al. (1997) · Nature · doi:10.1038/41483 · Cited by 3,529
Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock
Doolittle, R. F., Feng, D.-F., Tsang, S., Cho, G., & Little, E. (1996) · Science · doi:10.1126/science.271.5248.470 · Cited by 581
Cited by
The COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,430
Comparative assessment of large-scale data sets of protein–protein interactions
von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S., & Bork, P. (2002) · Nature · doi:10.1038/nature750 · Cited by 2,365
Self-citationSTRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
Snel, B. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.18.3442 · Cited by 1,249
Genome phylogeny based on gene content
Snel, B., Bork, P., & Huynen, M. A. (1999) · Nature Genetics · doi:10.1038/5052 · Cited by 716
Self-citationSTRING 7--recent developments in the integration and prediction of protein interactions
von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B., & Bork, P. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl825 · Cited by 665
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Metadata
- Authors
- Huynen, M. A., & Bork, P.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1998-05-26
- Volume
- 95
- Issue
- 11
- Pages
- 5849-5856
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2053501576
- Cited by
- 442
- References
- 4
- FWCI
- 8.44
- Type
- journal article
- Language
- en
- Open access
- green
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