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Evolution of gene order conservation in prokaryotes
Open accessAbstract
BACKGROUND: As more complete genomes are sequenced, conservation of gene order between different organisms is emerging as an informative property of the genomes. Conservation of gene order has been used for predicting function and functional interactions of proteins, as well as for studying the evolutionary relationships between genomes. The reasons for the maintenance of gene order are still not well understood, as the organization of the prokaryote genome into operons and lateral gene transfer cannot possibly account for all the instances of conservation found. Comprehensive studies of gene order are one way of elucidating the nature of these maintaining forces. RESULTS: Gene order is extensively conserved between closely related species, but rapidly becomes less conserved among more distantly related organisms, probably in a cooperative fashion. This trend could be universal in prokaryotic genomes, as archaeal genomes are likely to behave similarly to bacterial genomes. Gene order conservation could therefore be used as a valid phylogenetic measure to study relationships between species. Even between very distant species, remnants of gene order conservation exist in the form of highly conserved clusters of genes. This suggests the existence of selective processes that maintain the organization of these regions. Because the clusters often span more than one operon, common regulation probably cannot be invoked as the cause of the maintenance of gene order. CONCLUSIONS: Gene order conservation is a genomic measure that can be useful for studying relationships between prokaryotes and the evolutionary forces shaping their genomes. Gene organization is extensively conserved in some genomic regions, and further studies are needed to elucidate the reason for this conservation.
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“In conjunction with this, biological insight into genome locality (i.e., operonal or transcription unit structure) of related bacterial organisms can assist in clarifying the function of unknown JCVI-syn3A genes since genome architecture/gene locality is often significantly conserved in related organisms.47,48”
From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [47]
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“Gene clusters that appear resistant to dispersal include the ribosomal protein operon, the nuo operon (NADH dehydrogense), and the dcw cluster (66).”
Background
Metadata
- Authors
- Tamames, J.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Corresponding author
- Tamames, Javier
- ORCID
- Tamames, Javier
- Venue
- Genome Biology
- Published
- 2001-06-01
- Volume
- 2
- Issue
- 6
- Pages
- RESEARCH0020-RESEARCH0020
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC33396
- OpenAlex
- W1598176384
- Cited by
- 213
- References
- 29
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 3 · 2023: 3 · 2022: 5 · 2021: 5 · 2020: 8 · 2019: 4 · 2018: 4 · 2017: 5 · 2016: 8 · 2015: 3 · 2014: 12 · 2013: 12 · 2012: 8
- FWCI
- 3.27
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, other-oa)
- Funders
- Centro Nacional de Biotecnología
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Keywords
- gene order conservation, prokaryotic genomes, genome organization, gene clusters, operon, horizontal gene transfer, archaeal genomes, genome evolution, gene expression regulation
- MeSH terms
- Phylogeny, Genome, Bacterial, Conserved Sequence, Evolution, Molecular, Genome, Archaeal, Gene Order
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