ArticleNucleic acids research1989
Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons.
Article in Nucleic acids research, 1989. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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67 citing papers in PubMed, 168 citations in OpenAlex.
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- Mapping the evolutionary and translational landscape of antibiotic resistance genes in Elizabethkingia anopheles.Molecular genetics and genomics : MGG · 2026Article
- Dinucleotide preferences underlie apparent codon preference reversals in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.Polish journal of microbiology · 2024Article
- Article
- The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality.Molecular biology and evolution · 2022Article
- Genome-wide analysis of codon usage in sesame (Heliyon · 2022Article
- Analyses of Lysin-motif Receptor-like Kinase (Cells · 2021Article
- Analysis of codon usage bias of chloroplast genomes inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias.Molecular biology and evolution · 2021Article
- Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns.Genomics · 2021Article
- Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNABMC genomics · 2020Article
- Article
- Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements.Genome biology and evolution · 2016Article
- Expression-Linked Patterns of Codon Usage, Amino Acid Frequency, and Protein Length in the Basally Branching Arthropod Parasteatoda tepidariorum.Genome biology and evolution · 2016Article
- Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of Escherichia coli: Fitness and Epistatic Interactions.PloS one · 2016Article
- Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha.Bioinformatics and biology insights · 2016Article
- Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution.BMC evolutionary biology · 2014Article
- Evidence that natural selection on codon usage in Drosophila pseudoobscura varies across codons.G3 (Bethesda, Md.) · 2014Article
- Article
7 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Codon usage patterns in the slime mould Dictyostelium discoideum have been re-examined (a total of 58 genes have been analysed). Considering the extreme A + T-richness of this genome (G + C = 22%), there is a surprising degree of codon usage variation among genes. For example, G + C content at silent sites varies from less than 10% to greater than 30%. It was previously suggested [Warrick, H.M. and Spudich, J.A. (1988) Nucleic Acids Res. 16: 6617-6635] that highly expressed genes contain fewer 'optimal' codons than genes expressed at lower levels. However, it appears that the optimal codons were misidentified. Multivariate statistical analysis shows that the greatest variation among genes is in relative usage of a particular subset of codons (about one per amino acid), many of which are C-ending. We have identified these as optimal codons, since (i) their frequency is positively correlated with gene expression level, and (ii) there is a strong mutation bias in this genome towards A and T nucleotides. Thus, codon usage in D. discoideum can be explained by a balance between the forces of mutational bias and translational selection.
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