ArticleJournal of molecular evolution2022
Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes.
Article in Journal of molecular evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 16 citations in OpenAlex.
- Article
- The Pan-Plastome of Walnuts (International journal of molecular sciences · 2026Article
- Comparative analysis of the complete mitochondrial and chloroplast genomes of Krascheninnikovia arborescens reveals its evolutionary features in Amaranthaceae.BMC plant biology · 2026Article
- Complete chloroplast genomes of four Triumfetta species obtained from herbarium specimens: comparative analysis and identification of a synapomorphic inversion.Scientific reports · 2026Article
- Analysis and comparison of chloroplast genome codon usage patterns in five accessions of Toxicodendron vernicifluum.BMC genomics · 2026Article
- Comparative chloroplast genomics clarifies the taxonomic status and supports molecular identification ofFrontiers in plant science · 2026Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae.Functional & integrative genomics · 2024Article
- Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias.Acta biochimica Polonica · 2024Article
- Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory.Molecular biology and evolution · 2023Article
- Article
- Article
- Article
- Do Noncoding and Coding Sites in Angiosperm Chloroplast DNA Have Different Mutation Processes?Genes · 2023Article
- Complete chloroplast genome sequence ofComparative cytogenetics · 2023Article
- Comprehensive Analysis of Codon Usage inGenes · 2022Article
- Substitution rate heterogeneity across hexanucleotide contexts in noncoding chloroplast DNA.G3 (Bethesda, Md.) · 2022Article
- Article
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Authors and funding
1 author at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Two competing proposals about the degree to which selection affects codon usage of angiosperm chloroplast genes are examined. The first, based on observations that codon usage does not match expectations under the naïve assumption that base composition will be identical at all neutral sites, is that selection plays a significant role. The second is that codon usage is determined almost solely by mutation bias and drift, with selection influencing only one or two highly expressed genes, in particular psbA. First it is shown that, as a result of an influence of neighboring base composition on mutation dynamics, compositional biases are expected to be widely divergent at different sites in the absence of selection. The observed mutation properties are then used to predict expected neutral codon usage biases and to show that observed deviations from the naïve expectations are in fact expected given the context-dependent mutational dynamics. It is also shown that there is a match between the observed and expected codon usage when context effects are taken into consideration, with psbA being a notable exception. Overall, the data support the model that selection is not a widespread factor affecting the codon usage of angiosperm chloroplast genes and highlight the need to have an accurate model of mutational dynamics.
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