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Codon Usage Pattern of Genes Involved in Central Nervous System

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Abstract

Codon usage bias (CUB) is the non-uniform usage of synonymous codons in which some codons are more preferred to others in the transcript. Analysis of codon usage bias has applications in understanding the basics of molecular biology, genetics, gene expression, and molecular evolution. To understand the patterns of codon usage in genes involved in the central nervous system (CNS), we used bioinformatic approaches to analyze the protein-coding sequences of genes involved in the CNS. The improved effective number of codons (ENC) suggested that the overall codon usage bias was low. The relative synonymous codon usage (RSCU) revealed that the most frequently occurring codons had a G or C at the third codon position. The codons namely TCC, AGC, CTG, CAG, CGC, ATC, ACC, GTG, GCC, GGC, and CGG (average RSCU > 1.6) were over-represented. Both mutation pressure and natural selection might affect the codon usage pattern as evident from correspondence and parity plot analyses. The overall GC content (59.93) was higher than AT content, i.e., genes were GC-rich. The correlation of GC12 with GC3 suggested that mutation pressure might affect the codon usage pattern.

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Acknowledgements

The authors are thankful to Assam University, Silchar, Assam, India, for providing necessary facilities.

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Unfunded: The work was not supported by any national or international organization.

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Authors and Affiliations

  1. Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, Assam, 788150, India

    Arif Uddin

  2. Department of Biotechnology, Assam University, Silchar, Assam, 788011, India

    Supriyo Chakraborty

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  1. Arif Uddin
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  2. Supriyo Chakraborty
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Correspondence to Arif Uddin or Supriyo Chakraborty.

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Uddin, A., Chakraborty, S. Codon Usage Pattern of Genes Involved in Central Nervous System. Mol Neurobiol 56, 1737–1748 (2019). https://doi.org/10.1007/s12035-018-1173-y

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