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Analysis of synonymous codon usage in the VP2 protein gene of infectious bursal disease virus

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Abstract

Infectious bursal disease virus (IBDV) is an important poultry pathogen. The VP2 protein of IBDV is the major host-protective immunogen. Although the functions of the VP2 protein have been well studied, the factors shaping synonymous codon usage bias and nucleotide composition in the VP2 gene have not yet been reported. In the present study, we have analyzed the relative synonymous codon usage and effective number of codons (ENC) using 69 IBDV VP2 genes. The major trend in codon usage variation was studied using correspondence analysis. The plot of ENC values and GC3s as well as the correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in the VP2 gene. In addition, other factors, such as the aromaticity, hydrophobicity and aliphatic index also influence the codon usage variation of the VP2 gene. This study represents a comprehensive analysis of IBDV VP2 gene codon usage patterns and provides a basic understanding of the codon usage bias.

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Acknowledgments

We are thankful to Mr. Rohit Koul at Seasia Infotech for proofreading the manuscript. The IBDV research in our laboratory is currently supported by an IITG start-up grant, and partly by the Department of Biotechnology (NER-BPMC/2013/AAB21).

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  1. Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India

    Chandra Shekhar Kumar, Nazia M. J. Hazarika & Sachin Kumar

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  1. Chandra Shekhar Kumar
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  2. Nazia M. J. Hazarika
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  3. Sachin Kumar
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Correspondence to Sachin Kumar.

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Kumar, C.S., Hazarika, N.M.J. & Kumar, S. Analysis of synonymous codon usage in the VP2 protein gene of infectious bursal disease virus. Arch Virol 160, 2359–2366 (2015). https://doi.org/10.1007/s00705-015-2505-0

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