ArticleBMC genomic data2023
Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species.
Article in BMC genomic data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 48 citations in OpenAlex.
- Rubus chingii chloroplast genome sequences: a comparative analysis with other Rubus L.chloroplast genomes.BMC genomics · 2026Article
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- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- Integrative chloroplast genomics of Polygonaceae: evolutionary dynamics, codon optimization, and phylogenetic resolution.BMC plant biology · 2026Article
- Comprehensive analysis of 73 Aconitum chloroplast genomes reveals their structure, codon usage bias, and phylogenetic relationships within family Ranunculaceae.Scientific reports · 2026Article
- Analysis and comparison of chloroplast genome codon usage patterns in five accessions of Toxicodendron vernicifluum.BMC genomics · 2026Article
- Organellar genome evolution in Camellia tianeensis (Theaceae): comparative insights into RNA editing, codon usage, and DNA transfer between chloroplast and mitochondrion.BMC genomics · 2026Article
- Article
- Chloroplast genome comparative analysis and phylogenetic relationships of 15 Syringa species (Oleaceae).Genetics and molecular biology · 2026Article
- Comparative analysis of morphology and chloroplast genomes in endangered plantFrontiers in plant science · 2026Article
- Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Integrative genomic and machine learning approaches reveal evolutionary signatures in the winged bean mitochondrial genome.BMC plant biology · 2025Article
- Comparative plastome analysis of Schweinfurthia papilionacea and Schweinfurthia imbricata clarifying their taxonomic position in Lamiales.Scientific reports · 2025Article
- Mitochondrial codon usage bias and novel phylogenetic insights: implications for taxonomic reevaluation of seven Xylotini species (Diptera, Syrphidae, Eristalinae).BMC genomics · 2025Article
- Comparative mitogenomics reveals evolutionary drivers of Strongyloidea nematodes dwelling in gastrointestinal tract.BMC genomics · 2025Article
- Comparative Genomics and Phylogenetics of Chloroplasts Reveal Lower Rates of Genetic Variation in Mango (Ecology and evolution · 2025Article
- Phylogeny and evolutionary dynamics of the Rubia genus based on the chloroplast genome of Rubia tibetica.Scientific reports · 2025Article
- Decoding the Chloroplast Genome of Bitterwood (Ecology and evolution · 2025Article
- Analysis of synonymous codon usage bias of Lassa virus.Virus research · 2025Article
- The organelle genomes of the endangered seagrassFrontiers in plant science · 2025Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Phenomenon of codon usage bias exists in the genomes of prokaryotes and eukaryotes. The codon usage pattern is affected by environmental factors, base mutation, gene flow and gene expression level, among which natural selection and mutation pressure are the main factors. The study of codon preference is an effective method to analyze the source of evolutionary driving forces in organisms. Epimedium species are perennial herbs with ornamental and medicinal value distributed worldwide. The chloroplast genome is self-replicating and maternally inherited which is usually used to study species evolution, gene expression and genetic transformation.
resultsThe results suggested that chloroplast genomes of Epimedium species preferred to use codons ending with A/U. 17 common high-frequency codons and 2-6 optimal codons were found in the chloroplast genomes of Epimedium species, respectively. According to the ENc-plot, PR2-plot and neutrality-plot, the formation of codon preference in Epimedium was affected by multiple factors, and natural selection was the dominant factor. By comparing the codon usage frequency with 4 common model organisms, it was found that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae were suitable exogenous expression receptors.
conclusionThe evolutionary driving force in the chloroplast genomes of 10 Epimedium species probably comes from mutation pressure. Our results provide an important theoretical basis for evolutionary analysis and transgenic research of chloroplast genes.
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