ArticleEvolutionary bioinformatics online2015
Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity.
Article in Evolutionary bioinformatics online, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 20 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
- Complete Chloroplast Genome ofGenes · 2024Article
- Codon usage bias.Molecular biology reports · 2022Review
- Analysis of codon usage bias of chloroplast genomes inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat.Frontiers in genetics · 2021Article
- Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat.PloS one · 2020Article
- Codon usage by chloroplast gene is bias inJournal of genetics · 2020Article
- Transit From Autotrophism to Heterotrophism: Sequence Variation and Evolution of Chloroplast Genomes in Orobanchaceae Species.Frontiers in genetics · 2020Article
- The Complete Chloroplast Genome of Heimia myrtifolia and Comparative Analysis within Myrtales.Molecules (Basel, Switzerland) · 2018Article
- Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats.3 Biotech · 2017Article
- Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution.PloS one · 2015Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation-induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.
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