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Gene sequences useful for predicting relatedness of whole genomes in bacteria
Abstract
Thirty-two protein-encoding genes that are distributed widely among bacterial genomes were tested for the potential usefulness of their DNA sequences in assigning bacterial strains to species. From publicly available data, it was possible to make 49 pairwise comparisons of whole bacterial genomes that were related at the genus or subgenus level. DNA sequence identity scores for eight of the genes correlated strongly with overall sequence identity scores for the genome pairs. Even single-gene alignments could predict overall genome relatedness with a high degree of precision and accuracy. Predictions could be refined further by including two or three genes in the analysis. The proposal that sequence analysis of a small set of protein-encoding genes could reliably assign novel strains or isolates to bacterial species is strongly supported.
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Cites
Fast algorithms for large-scale genome alignment and comparison
Delcher, A. L. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2478 · Cited by 1,036
Cited by
Thompson, F. L., Iida, T., & Swings, J. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.3.403-431.2004 · Cited by 1,240
Re-evaluating prokaryotic species
Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E., de Peer, Y. V., Vandamme, P., Thompson, F. L., et al. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1236 · Cited by 1,122
Martens, M., Dawyndt, P., Coopman, R., Gillis, M., De Vos, P., & Willems, A. (2008) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.65392-0 · Cited by 416
Naser, S. M., Thompson, F. L., Hoste, B., Gevers, D., Dawyndt, P., Vancanneyt, M., & Swings, J. (2005) · Microbiology · doi:10.1099/mic.0.27840-0 · Cited by 409
Fuzzy species among recombinogenic bacteria
Hanage, W. P., Fraser, C., & Spratt, B. G. (2005) · BMC Biology · doi:10.1186/1741-7007-3-6 · Cited by 318
Metadata
- Authors
- Zeigler, D. R.
- Venue
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Publisher
- Microbiology Society
- Published
- 2003-11-01
- Volume
- 53
- Issue
- 6
- Pages
- 1893-1900
- ISSN
- 1466-5026 (ISSN-L)
- 1466-5034
- OpenAlex
- W2109268199
- Cited by
- 341
- References
- 1
- FWCI
- 4.72
- Type
- journal article
- Language
- en
- Open access
- closed
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- Zeigler, D. R. (2003). Gene sequences useful for predicting relatedness of whole genomes in bacteria. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. https://doi.org/10.1099/ijs.0.02713-0
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
