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Codon usage vis-a-vis start and stop codon context analysis of three dicot species

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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 the usage 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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Acknowledgements

Authors are grateful to the University Grants Commission, New Delhi, India, for providing UGC-BSR Fellowship to carry out this research work. Authors are also grateful to the Assam University, Silchar, Assam, India for providing the research facility.

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Authors and Affiliations

  1. Department of Biotechnology, Assam University, Silchar,  788 011, India

    Prosenjit Paul, Arup Kumar Malakar & Supriyo Chakraborty

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  1. Prosenjit Paul
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  2. Arup Kumar Malakar
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Correspondence to Supriyo Chakraborty.

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Corresponding editor: Umesh Varshney

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Paul, P., Malakar, A.K. & Chakraborty, S. Codon usage vis-a-vis start and stop codon context analysis of three dicot species. J Genet 97, 97–107 (2018). https://doi.org/10.1007/s12041-018-0892-1

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