ArticlePlanta2020
Analysis of codon usage bias of chloroplast genes in Oryza species : Codon usage of chloroplast genes in Oryza species.
Article in Planta, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 121 citations in OpenAlex.
- Comprehensive analysis of synonymous codon usage bias and evolutionary dynamics in the chloroplast genomes of eight Coptis species.Functional & integrative genomics · 2026Article
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- Codon usage patterns and phylogenetic analysis of chloroplast genomes reveal evolutionary insights into Asphodelaceae species.Scientific reports · 2026Article
- Comparative chloroplast genome analysis of Polygala species: insights into evolution, phylogeny, and DNA barcoding.Planta · 2026Article
- Integrative chloroplast genomics of Polygonaceae: evolutionary dynamics, codon optimization, and phylogenetic resolution.BMC plant biology · 2026Article
- Analysis and comparison of chloroplast genome codon usage patterns in five accessions of Toxicodendron vernicifluum.BMC genomics · 2026Article
- Pan-chloroplast genomes ofFrontiers in plant science · 2026Article
- Integrative chloroplast omics in citrus: computational insights into genomic structural adaptation and phylogenetic relationships from 35 species.Frontiers in plant science · 2026Article
- Complete Chloroplast Genome Characterization, and Phylogenetic Analyses of the Rare and Endangered PlantBiology · 2025Article
- Phylogenomic Analyses and DNA Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive Evolution.Ecology and evolution · 2025Article
- Comparative Genomics ofInternational journal of molecular sciences · 2025Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
- Mechanisms, detection, and impact of horizontal gene transfer in plant functional evolution.The Plant cell · 2025Review
- Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides.Biochemical genetics · 2025Article
- The complete plastome of the Antarctic moss Andreaea regularis (Andreaeaceae) and its comparative analyses within Bryophyta.BMC genomics · 2025Article
- Eight NewGenes · 2025Article
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- Codon-Usage Bias and Genomic Architecture of 79 Psoriasis-Susceptibility Genes: Implications for Expression Efficiency and Therapeutic Targeting.Psoriasis (Auckland, N.Z.) · 2025Article
- Complete chloroplast genomes of threeFrontiers in plant science · 2025Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MAIN
conclusionThe codon usage bias in chloroplast genes of Oryza species was low and AT rich. The pattern of codon usage was different among Oryza species and mainly influenced by mutation pressure and natural selection. Codon usage bias (CUB) is the unequal usage of synonymous codons in which some codons are more preferred to others in the coding sequences of genes. It shows a species-specific property. We studied the patterns of codon usage and the factors that influenced the CUB of protein-coding chloroplast (cp) genes in 18 Oryza species as no work was yet reported. The nucleotide composition analysis revealed that the overall GC content of cp genes in different species of Oryza was lower than 50%, i.e., Oryza cp genes were AT rich. Synonymous codon usage order (SCUO) suggested that CUB was weak in the cp genes of different Oryza species. A highly significant correlation was observed between overall nucleotides and its constituents at the third codon position suggesting that both, mutation pressure and natural selection, might influence the CUB. Correspondence analysis (COA) revealed that codon usage pattern differed across Oryza species. In the neutrality plot, a narrow range of GC3 distribution was recorded and some points were diagonally distributed in all the plots, suggesting that natural selection and mutation pressure might have influenced the CUB. The slope of the regression line was < 0.5, augmenting our inference that natural selection might have played a major role, while mutation pressure had a minor role in shaping the CUB of cp genes. The magnitudes of mutation pressure and natural selection on cp genes varied across Oryza species.
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