ArticleBMC genomics2013
Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 70 citations in OpenAlex.
- Nucleotide Combination Proportions Across Algae, Monocotyledons and Dicotyledons: Insights into Plant Genome Evolution.Plants (Basel, Switzerland) · 2026Article
- The chloroplast genome sequence and phylogenetic analysis of Rubia alata Wall and Rubia ovatifolia Z. Ying Zhang. (Rubiaceae).Molecular biology reports · 2024Article
- Chloroplast Genome Variation and Phylogenetic Relationships of Autochthonous Varieties ofInternational journal of molecular sciences · 2024Article
- New insights on the phylogeny, evolutionary history, and ecological adaptation mechanism in cycle-cup oaks based on chloroplast genomes.Ecology and evolution · 2024Article
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- The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice.International journal of molecular sciences · 2022Article
- The Chloroplast Genome of the Lichen PhotobiontGenes · 2022Article
- Characterization of the Chloroplast Genome ofGenes · 2022Article
- Alteration of synonymous codon usage bias accompanies polyploidization in wheat.Frontiers in genetics · 2022Article
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- Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L.BMC 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
- The Complete Chloroplast Genomes ofInternational journal of molecular sciences · 2019Article
- Evolutionary Consequences of DNA Methylation in a Basal Metazoan.Molecular biology and evolution · 2016Article
- Article
- Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes.Genome biology and evolution · 2015Article
- Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity.Evolutionary bioinformatics online · 2015Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEvidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. However, the relationship (if any) between SCUB and intron number as well as exon position is at present rather unclear.
resultsTo explore this relationship, the sequences of a set of genes containing between zero and nine introns was extracted from the published genome sequences of three algal species, one moss, one fern and six angiosperms (three monocotyledonous species and three dicotyledonous species). In the algal genomes, the frequency of synonymous codons of the form NNG/NNC (codons with G and C at the third position) was positively related to intron number, but that of NNA/NNT was inversely correlated; the opposite was the case in the land plant genomes. The frequency of NNC/NNG was higher and that of NNA/NNT lower in two terminal exons than in the interstitial exons in the land plant genes, but the rule showed to be opposite in the algal genes. SCUB patterns in the interstitial and two terminal exons mirror the different evolutionary relationships between these plant species, while the first exon shows the highest level of conservation is therefore concluded to be the one which experiences the heaviest selection pressure. The phenomenon of SCUB may also be related to DNA methylation induced conversion of CG to AT.
conclusionsThese data provide some evidence of linkage between SCUB, the evolution of introns and DNA methylation, which brings about a new perspective for understanding how genomic variation is created during plant evolution.
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