ArticlePloS one2014
Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea).
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed.
- From Codons to Protein Structure: Evolutionary Constraints of Mitochondrial Proteins in Corvides.Biology · 2026Article
- De novo mitogenome assembly and phylogenetic implications of the first Indian yak breed-Arunachali (Bos or Poephagus grunniens L.).Molecular biology reports · 2026Article
- Mitochondrial genomes of Dactylogyrus wunderi (Monopisthocotyla: Dactylogyridae): structural features, codon usage patterns, and phylogenetic implications.BMC genomics · 2026Article
- Article
- Synonymous but not silent: functional codon bias reveals decoupled mitonuclear evolution in parasitic worms.Bioinformatics advances · 2026Article
- Codon usage bias of low-risk human papillomavirus types 6 and 11.Antonie van Leeuwenhoek · 2025Article
- Codon Usage Pattern and its Influencing Factors for Mitochondrial CO Genes Among Different Subfamilies of Cerambycidae.Biochemical genetics · 2025Article
- A Review of the Newly Recorded GenusInsects · 2025Article
- Decoding codon usage in human papillomavirus type 59.Virus genes · 2025Article
- Genetic Characteristics and Phylogenetic Relationships of 18 Anchovy Species Based on Mitochondrial Genomes in the Seas Around China.Ecology and evolution · 2025Article
- Characterization and Phylogenetic Analysis of the Complete Mitogenomes ofJournal of fungi (Basel, Switzerland) · 2025Article
- Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.Polish journal of microbiology · 2024Article
- Comparative mitochondrial genomics of Thelebolaceae in Antarctica: insights into their extremophilic adaptations and evolutionary dynamics.IMA fungus · 2024Article
- SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome.International journal of molecular sciences · 2024Article
- Characterization, Codon Usage Pattern and Phylogenetic Implications of the Waterlily AphidInternational journal of molecular sciences · 2024Article
- Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.BMC genomics · 2024Article
- First report of the complete mitochondrial genome of 3 beetles (Coleoptera: Scarabaeidae) harming Gastrodia elata (Asparagales: Orchidaceae).Journal of insect science (Online) · 2024Article
- Pan-genome wide identification and analysis of theFrontiers in plant science · 2024Article
- Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa.Microorganisms · 2023Article
- Analysis of synonymous codon usage patterns in mitochondrial genomes of nineFrontiers in microbiology · 2023Article
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4 authors.
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Abstract
The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.
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