ReviewJournal of molecular evolution2016
The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.
Review in Journal of molecular evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 74 citations in OpenAlex.
- Comparative mitogenomics of freshwater snails of the genus Biomphalaria (Gastropoda: Planorbidae) and new insights into mitochondrial genome evolution in Hygrophila.BMC ecology and evolution · 2026Article
- Analysis and comparison of chloroplast genome codon usage patterns in five accessions of Toxicodendron vernicifluum.BMC genomics · 2026Article
- Synonymous codon usage defines functional gene families.BMC biology · 2026Article
- Genomic and physiological signatures of adaptation in pathogenic fungi.Nature communications · 2026Article
- RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU).BMC bioinformatics · 2025Article
- Compare Analysis of Codon Usage Bias of Nuclear Genome in Eight Sapindaceae Species.International journal of molecular sciences · 2024Article
- Article
- SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome.International journal of molecular sciences · 2024Article
- Dynamic evolution of peste des petits ruminants virus in sheep and goat hosts across India reveals the swift surge of F gene.Virusdisease · 2024Article
- The RdRp genotyping of SARS-CoV-2 isolated from patients with different clinical spectrum of COVID-19.BMC infectious diseases · 2024Article
- Molecular Mechanisms and the Significance of Synonymous Mutations.Biomolecules · 2024Review
- Article
- Chromosome-Level Analysis of theBiology · 2023Article
- Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.Virology · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Pan-cancer analysis of co-occurring mutations in RAD52 and the BRCA1-BRCA2-PALB2 axis in human cancers.PloS one · 2022Article
- Article
- Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus.Pathogens (Basel, Switzerland) · 2021Article
- Arginine Depletion in Human Cancers.Cancers · 2021Article
- Analysis of Codon Usage Patterns inGenes · 2021Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Some mutations in gene coding regions exchange one synonymous codon for another, and thus do not alter the amino acid sequence of the encoded protein. Even though they are often called 'silent,' these mutations may exhibit a plethora of effects on the living cell. Therefore, they are often selected during evolution, causing synonymous codon usage biases in genomes. Comparative analyses of bacterial, archaeal, fungal, and human cancer genomes have found many links between a gene's biological role and the accrual of synonymous mutations during evolution. In particular, highly expressed genes in certain functional categories are enriched with optimal codons, which are decoded by the abundant tRNAs, thus enhancing the speed and accuracy of the translating ribosome. The set of genes exhibiting codon adaptation differs between genomes, and these differences show robust associations to organismal phenotypes. In addition to selection for translation efficiency, other distinct codon bias patterns have been found in: amino acid starvation genes, cyclically expressed genes, tissue-specific genes in animals and plants, oxidative stress response genes, cellular differentiation genes, and oncogenes. In addition, genomes of organisms harboring tRNA modifications exhibit particular codon preferences. The evolutionary trace of codon bias patterns across orthologous genes may be examined to learn about a gene's relevance to various phenotypes, or, more generally, its function in the cell.
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