ArticleMolecular biology and evolution2021
Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 33 citations in OpenAlex.
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- Characterization of the mitochondrial genome of the aquatic vegetable Eleocharis dulcis (Burm. f.) Trin. ex Hensch.: the first representative of genus Eleocharis with evolutionary insights in Cyperaceae.BMC plant biology · 2026Article
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- Protein language models reveal evolutionary constraints on synonymous codon choice.bioRxiv : the preprint server for biology · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Variation in the fitness impact of translationally optimal codons among animals.Genome research · 2025Article
- Assembly and comparative analysis of the complete mitochondrial genome of Lactuca sativa var. ramosa Hort.Scientific reports · 2025Article
- Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.Current genomics · 2025Review
- Comparative analysis of chloroplast genomes on Meliaceae species: insights into the evolution and species identification.Frontiers in plant science · 2025Article
- Compare Analysis of Codon Usage Bias of Nuclear Genome in Eight Sapindaceae Species.International journal of molecular sciences · 2024Article
- Selection on synonymous codon usage in soybean (Glycine max) WRKY genes.Scientific reports · 2024Article
- Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the EndangeredGenes · 2024Article
- The Patterns of Codon Usage between Chordates and Arthropods are Different but Co-evolving with Mutational Biases.Molecular biology and evolution · 2024Article
- Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene.BMC ecology and evolution · 2024Article
- Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases.Molecular biology and evolution · 2023Article
- Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory.Molecular biology and evolution · 2023Article
- Growth-dependent gene expression variation influences the strength of codon usage biases.bioRxiv : the preprint server for biology · 2023Article
- Variation in synonymous evolutionary rates in the SARS-CoV-2 genome.Frontiers in microbiology · 2023Article
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
Abstract
Alternative synonymous codons are often used at unequal frequencies. Classically, studies of such codon usage bias (CUB) attempted to separate the impact of neutral from selective forces by assuming that deviations from a predicted neutral equilibrium capture selection. However, GC-biased gene conversion (gBGC) can also cause deviation from a neutral null. Alternatively, selection has been inferred from CUB in highly expressed genes, but the accuracy of this approach has not been extensively tested, and gBGC can interfere with such extrapolations (e.g., if expression and gene conversion rates covary). It is therefore critical to examine deviations from a mutational null in a species with no gBGC. To achieve this goal, we implement such an analysis in the highly AT rich genome of Dictyostelium discoideum, where we find no evidence of gBGC. We infer neutral CUB under mutational equilibrium to quantify "adaptive codon preference," a nontautologous genome wide quantitative measure of the relative selection strength driving CUB. We observe signatures of purifying selection consistent with selection favoring adaptive codon preference. Preferred codons are not GC rich, underscoring the independence from gBGC. Expression-associated "preference" largely matches adaptive codon preference but does not wholly capture the influence of selection shaping patterns across all genes, suggesting selective constraints associated specifically with high expression. We observe patterns consistent with effects on mRNA translation and stability shaping adaptive codon preference. Thus, our approach to quantifying adaptive codon preference provides a framework for inferring the sources of selection that shape CUB across different contexts within the genome.
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