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Codon usage and amino acid usage influence genes expression level

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Abstract

Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.

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Acknowledgements

The authors are grateful to the University Grants Commission, New Delhi, India, for providing a UGC-BSR Fellowship to carry out this research work. We 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, 788011, Assam, 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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  3. Supriyo Chakraborty
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Contributions

P.P carried out all analyses, conceived the idea, analyzed the data and wrote the paper. A.K.M prepared the figures and tables. S.C prepared the software for analysis and edited the manuscript. All authors reviewed the manuscript.

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Correspondence to Supriyo Chakraborty.

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The authors did not avail any financial assistance from any source in undertaking the present study.

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The authors declare that there is no conflict of interests regarding the publication of this paper.

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Paul, P., Malakar, A.K. & Chakraborty, S. Codon usage and amino acid usage influence genes expression level. Genetica 146, 53–63 (2018). https://doi.org/10.1007/s10709-017-9996-4

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