ArticleNucleic acids research2005
Variation in the strength of selected codon usage bias among bacteria.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 224 papers.
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Who cites it
224 citing papers in PubMed.
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- Hierarchical evolution of the proteobacterial essential chaperone SecB reveals non-neutral synonymous evolution under extreme purifying selection.Molecular genetics and genomics : MGG · 2026Article
- Multipartite mitochondrial genome evolution in Halophila seagrasses: repeat-driven structural plasticity and selection signatures of marine adaptation.BMC plant biology · 2026Article
- Codon bias variation in Staphylococcus aureus.PloS one · 2026Article
- Codon Optimization is Required to Express Fluorogenic Reporter Proteins in Lactococcus lactis.Molecular biotechnology · 2025Article
- Cell type-specific purifying selection of synonymous mitochondrial DNA variation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comparative analysis of plastome structure in Sphagnum species from China.BMC genomics · 2025Article
- A model of Hill-Robertson interference caused by purifying selection in a nonrecombining genome.Genetics · 2025Article
- Article
- Variation in the fitness impact of translationally optimal codons among animals.Genome research · 2025Article
- Decoding Codon Usage Patterns in High-Risk Human Papillomavirus Genomes: A Comprehensive Analysis.Current microbiology · 2025Article
- Comprehensive analysis of the mitochondrial genome in lichen genusFrontiers in microbiology · 2025Article
- Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.Polish journal of microbiology · 2024Article
- A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.Science advances · 2024Article
- The Effect of the Presence and Absence of DNA Repair Genes on the Rate and Pattern of Mutation in Bacteria.Genome biology and evolution · 2024Article
164 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. However, in other species selection appears to have been ineffective. Here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. The approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. The strength of selected codon usage bias, S, is found to vary substantially among species; in 30% of the genomes examined, there was no significant evidence that selection had been effective. Values of S are highly positively correlated with both the number of rRNA operons and the number of tRNA genes. These results are consistent with the hypothesis that species exposed to selection for rapid growth have more rRNA operons, more tRNA genes and more strongly selected codon usage bias. For example, Clostridium perfringens, the species with the highest value of S, can have a generation time as short as 7 min.
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