ArticleJournal of genetics2018
Codon usage vis-a-vis start and stop codon context analysis of three dicot species.
Article in Journal of genetics, 2018. 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.
- Article
- Integrative genomic and machine learning approaches reveal evolutionary signatures in the winged bean mitochondrial genome.BMC plant biology · 2025Article
- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Comprehensive analysis of complete chloroplast genome sequence of Morina L.Scientific reports · 2025Article
- An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea.BMC genomic data · 2023Article
- The genome of Candidatus phytoplasma ziziphi provides insights into their biological characteristics.BMC plant biology · 2023Article
- An investigation of codon usage pattern analysis in pancreatitis associated genes.BMC genomic data · 2022Article
- Codon usage patterns across seven Rosales species.BMC plant biology · 2022Article
- Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens.Molecular genetics and genomics : MGG · 2021Article
- Codon usage bias and dinucleotide preference in 29 Drosophila species.G3 (Bethesda, Md.) · 2021Article
- Genomewide comparative analysis of codon usage bias in three sequencedJournal of genetics · 2021Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To understand the variation in genomic composition and its effect on codon usage, we performed the comparative analysis of codon usage and nucleotide usage in the genes of three dicots, Glycine max, Arabidopsis thaliana and Medicago truncatula. The dicot genes were found to be A/T rich and have predominantly A-ending and/or T-ending codons. GC3s directly mimic theusage pattern of global GC content. Relative synonymous codon usage analysis suggests that the high usage frequency of A/T over G/C mononucleotide containing codons in AT-rich dicot genome is due to compositional constraint as a factor of codon usage bias. Odds ratio analysis identified the dinucleotides TpG, TpC, GpA, CpA and CpT as over-represented, where, CpG and TpA as under-represented dinucleotides. The results of (NcExp-NcObs)/NcExp plot suggests that selection pressure other than mutation played a significant role in influencing the pattern of codon usage in these dicots. PR2 analysis revealed the significant role of selection pressure on codon usage. Analysis of varience on codon usage at start and stop site showed variation in codon selection in these sites. This study provides evidence that the dicot genes were subjected to compositional selection pressure.
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Registered trials
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