ArticleGenetics2001
Selection at the amino acid level can influence synonymous codon usage: implications for the study of codon adaptation in plastid genes.
Article in Genetics, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost.Protein science : a publication of the Protein Society · 2025Article
- The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes.International journal of molecular sciences · 2023Article
- No evidence for widespread positive selection on double substitutions within codons in primates and yeasts.Frontiers in genetics · 2022Article
- Are Nonsynonymous Transversions Generally More Deleterious than Nonsynonymous Transitions?Molecular biology and evolution · 2021Article
- New Insight into Parrots' Mitogenomes Indicates That Their Ancestor Contained a Duplicated Region.Molecular biology and evolution · 2018Article
- The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons.G3 (Bethesda, Md.) · 2017Article
- Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.Computational and structural biotechnology journal · 2017Article
- Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity.Evolutionary bioinformatics online · 2015Article
- Article
- Synonymous but not the same: the causes and consequences of codon bias.Nature reviews. Genetics · 2011Review
- Neutral evolution of synonymous base composition in the Brassicaceae.Journal of molecular evolution · 2007Article
- Determination of mutation trend in proteins by means of translation probability between RNA codes and mutated amino acids.Biochemical and biophysical research communications · 2005Article
- Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.BMC bioinformatics · 2004Article
- Evolutionary patterns of codon usage in the chloroplast gene rbcL.Journal of molecular evolution · 2003Article
- Genomes at the interface between bacteria and organelles.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2003Review
Corrections and comments
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Authors and funding
1 author.
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Abstract
A previously employed method that uses the composition of noncoding DNA as the basis of a test for selection between synonymous codons in plastid genes is reevaluated. The test requires the assumption that in the absence of selective differences between synonymous codons the composition of silent sites in coding sequences will match the composition of noncoding sites. It is demonstrated here that this assumption is not necessarily true and, more generally, that using compositional properties to draw inferences about selection on silent changes in coding sequences is much more problematic than commonly assumed. This is so because selection on nonsynonymous changes can influence the composition of synonymous sites (i.e., codon usage) in a complex manner, meaning that the composition biases of different silent sites, including neutral noncoding DNA, are not comparable. These findings also draw into question the commonly utilized method of investigating how selection to increase translation accuracy influences codon usage. The work then focuses on implications for studies that assess codon adaptation, which is selection on codon usage to enhance translation rate, in plastid genes. A new test that does not require the use of noncoding DNA is proposed and applied. The results of this test suggest that far fewer plastid genes display codon adaptation than previously thought.
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