ArticleMolecular biology and evolution2019
Elucidation of Codon Usage Signatures across the Domains of Life.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Association of hybridization and genome doubling with codon usage landscapes in the subgenomes of bread wheat.Frontiers in plant science · 2026Article
- Uncovering position-specific patterns in codon and codon-pair usage in candidate genes associated with blood coagulation diseases.NAR genomics and bioinformatics · 2025Article
- Preparation and Immunological Efficacy Evaluation of mRNA Vaccines Targeting the Spike Protein of Bovine Coronavirus.Vaccines · 2025Article
- Near-cognate tRNAs dominate codon decoding times in simulated ribosomes.Nucleic acids research · 2025Article
- Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution.Viruses · 2025Review
- Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage.Journal of molecular evolution · 2025Article
- Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics.Scientific reports · 2025Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Article
- Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli.Genome biology and evolution · 2024Article
- The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder.bioRxiv : the preprint server for biology · 2024Article
- Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene.BMC ecology and evolution · 2024Article
- Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases.Annals of medicine and surgery (2012) · 2024Article
- Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies.Genome biology and evolution · 2023Article
- Protein expression/secretion boost by a novel unique 21-mer cis-regulatory motif (Exin21) via mRNA stabilization.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Article
- On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes.RNA biology · 2023Article
- Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance.BMC genomics · 2022Article
- An overview of dinucleotide and codon usage in all viruses.Archives of virology · 2022Review
- Comparative Genomic Analysis Reveals Potential Pathogenicity and Slow-Growth Characteristics of GenusMicrobiology spectrum · 2022Article
- Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.Virology · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being "synonymous," these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutational drift, is the major determinant of variation across species. Here, we find that in addition to GC content, interspecies codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding and show that domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain of life with high accuracy. We then wondered whether the inclusion of codon usage codon autocorrelation patterns, which reflects the nonrandom distribution of codon occurrences throughout a transcript, might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to previous reports. Instead, our results suggest that codon autocorrelation patterns are a by-product of codon optimality throughout a sequence, where highly expressed genes display autocorrelated "optimal" codons, whereas lowly expressed genes display autocorrelated "nonoptimal" codons.
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