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Updated: Feb 11, 2026
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Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
Published on: June 24, 2019
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Codon usage vis-a-vis start and stop codon context analysis of three dicot species
Prosenjit Paul1, Arup Kumar Malakar, Supriyo Chakraborty
1Department of Biotechnology, Assam University, Silchar 788 011, India. supriyoch2008@gmail.com.
Journal of Genetics
|April 19, 2018
Summary
Dicot genes in Glycine max, Arabidopsis thaliana, and Medicago truncatula show A/T richness and codon usage bias due to compositional constraints. Selection pressure significantly influences codon usage patterns in these plant genomes.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Codon usage bias influences gene expression and protein synthesis.
- Genomic composition significantly impacts evolutionary trajectories of genes.
Purpose of the Study:
- To investigate codon usage patterns and genomic composition in three dicot species.
- To determine the factors driving codon usage bias in dicot genes.
Main Methods:
- Comparative analysis of codon usage and nucleotide composition.
- Relative synonymous codon usage (RSCU) analysis.
- Odds ratio analysis for dinucleotide frequencies.
- Analysis of effective number of codons (Nc) and PR2 analysis.
Main Results:
- Dicot genes are AT-rich with a preference for A/T-ending codons.
- GC3 content mirrors global GC content, indicating compositional constraints.
- Specific dinucleotides (TpG, TpC, GpA, CpA, CpT) are over-represented, while CpG and TpA are under-represented.
- Selection pressure, beyond mutation, significantly shapes codon usage.
Conclusions:
- Compositional constraints are a major factor in codon usage bias in AT-rich dicot genomes.
- Selection pressure plays a crucial role in influencing codon usage patterns.
- Variations in codon selection occur at gene start and stop sites.
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