ArticleBMC evolutionary biology2008
Molecular evolution of synonymous codon usage in Populus.
Article in BMC evolutionary biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
- Genome-wide association study and KASP development for growth and leaf traits in Populus deltoides.BMC genomics · 2026Article
- Analysis of Chloroplast Genome Characteristics and Codon Usage Bias ofCurrent issues in molecular biology · 2026Article
- Evidence for Non-optimal Codon Choice in Highly Transcribed Sex-Biased Genes of Drosophila melanogaster.Genome biology and evolution · 2026Article
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- Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species.Functional & integrative genomics · 2024Article
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- Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa.Microorganisms · 2023Article
- Characterization and Comparative Analysis of Chloroplast Genomes of Medicinal HerbInternational journal of molecular sciences · 2023Article
- Analysis of Codon Usage Bias in Xyloglucan Endotransglycosylase (XET) Genes.International journal of molecular sciences · 2023Article
- The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus.Virus evolution · 2023Article
- Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae).BMC plant biology · 2022Article
- Globally Relaxed Selection and Local Adaptation in Boechera stricta.Genome biology and evolution · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes.BMC genomics · 2021Article
- Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae).Scientific reports · 2020Article
- Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study.PloS one · 2020Article
- Evidence of multifaceted functions of codon usage in translation within the model beetle Tribolium castaneum.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- A Novel Gene Coding γ-Aminobutyric Acid Transporter May Improve the Tolerance ofFrontiers in plant science · 2019Article
- Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors.BMC plant biology · 2018Article
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Abstract
backgroundEvolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes.
resultsI examined the evolution of synonymous codons using EST data from five species of Populus. Data on relative synonymous codon usage in genes with high and low gene expression were used to identify 25 codons from 18 different amino acids that were deemed to be preferred codons across all five species. All five species show significant correlations between codon bias and gene expression, independent of base composition, thus indicating that translational selection has shaped synonymous codon usage. Using a set of 158 orthologous genes I detected an excess of unpreferred to preferred (U --> P) mutations in two lineages, P. tremula and P. deltoides. Maximum likelihood estimates of the strength of selection acting on synonymous codons was also significantly greater than zero in P. tremula, with the ML estimate of 4Nes = 0.720.
conclusionThe data is consistent with weak selection on preferred codons in all five species. There is also evidence suggesting that selection on synonymous codons has increased in P. tremula. Although the reasons for the increase in selection on codon usage in the P. tremula lineage are not clear, one possible explanation is an increase in the effective population size in P. tremula.
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