ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
New insights into the interplay between codon bias determinants in plants.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Assembly and phylogenetic analysis of the mitochondrial genome of the Cyclocarya paliurus.Functional & integrative genomics · 2026Article
- Phylogenomic discordance among plastid genes in endangered Maltese Limonium.Scientific reports · 2026Article
- Codon usage patterns and phylogenetic analysis of chloroplast genomes reveal evolutionary insights into Asphodelaceae species.Scientific reports · 2026Article
- Comprehensive Codon Usage Analysis Across Diverse Plant Lineages.Biochemical genetics · 2026Article
- Phylogenomic Analyses and DNA Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive Evolution.Ecology and evolution · 2025Article
- The evolution of the aquaporin gene family and drought tolerance mechanisms in green plants.Horticulture research · 2025Article
- A novel recombinant CRISPR/Cas9 vector system for genome editing in plants.Transgenic research · 2025Article
- Comparative plastome analysis reveals evolutionary dynamics and codon usage patterns in Bidens (Asteraceae).Functional & integrative genomics · 2025Article
- Article
- Selection on synonymous codon usage in soybean (Glycine max) WRKY genes.Scientific reports · 2024Article
- Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina.BMC genomic data · 2024Article
- Comparative chloroplast genomics and insights into the molecular evolution of Tanaecium (Bignonieae, Bignoniaceae).Scientific reports · 2023Article
- Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species.BMC genomic data · 2023Article
- Genome-wide identification and comparative evolutionary analysis of sorbitol metabolism pathway genes in four Rosaceae species and three model plants.BMC plant biology · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Article
- Comprehensive analysis of coding sequence architecture features and gene expression inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Article
- Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae).Scientific reports · 2020Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.
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