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Codon usage bias

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Abstract

Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.

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Fig. 1
Fig. 2
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Fig. 4

Major factors affecting codon usage bias in organisms such as GC content of genome, population size, gene expression level, protein length, codon position and context, tRNA abundance and interactions and mRNA structure are diagrammatically indicated. tRNA interactions are classified into frequency bias, co-occurence bias and pair bias. E, P and A indicate exit, peptide and amino acid sites in the ribosomes. The tRNA interactions were modified and redrawn from [1]

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Data Availability

Not Applicable. All data are presented in the manuscript.

Code availability

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Acknowledgements

Sujatha Thankeswaran Parvathy thanks Indian Council of Agricultural Research, New Delhi and Centre for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore for the support. The topic was part of the postgraduation (MSc) course work of Sujatha Thankeswaran Parvathy at TNAU, Coimbatore. We immensely thank the esteemed reviewers and editorial board of the journal for the invaluable, critical comments and suggestions which helped us to improve the manuscript.

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  1. ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834010, India

    Sujatha Thankeswaran Parvathy & Vijaipal Bhadana

  2. Department of Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India

    Varatharajalu Udayasuriyan

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  1. Sujatha Thankeswaran Parvathy
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  2. Varatharajalu Udayasuriyan
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STP has performed the literature search, compilation, drafting, preparation or writing and revision of the manuscript. VU has provided valuable inputs in conceptualizing, correcting and revision of the manuscript. VPB has contributed to fine-tuning of the manuscript.

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Parvathy, S.T., Udayasuriyan, V. & Bhadana, V. Codon usage bias. Mol Biol Rep 49, 539–565 (2022). https://doi.org/10.1007/s11033-021-06749-4

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