Bioinformatics study involving characterization of synonymous codon usage bias in the duck enteritis virus glycoprotein D (gD) gene

Abstract

The aim of the study was to identify the codon usage bias between the newly identified Duck Enteritis Virus (DEV) gD gene (GenBank accession No. KC915041) and the gD like gene of 23 other reference herpesviruses. The codon usage bias analysis of gD gene of DEV may improve our understanding of the evolution and pathogenesis of DEV and provide a basis for understanding the relevant mechanism for biased usage of synonymous codons; and for selecting appropriate heterologous expression systems to improve the expression of target genes. The results showed that codon of gD gene of DEV was having strong bias towards the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed; and the effective number of codons used in a gene plot revealed that the genetic heterogeneity in gD gene of herpesviruses was constrained by the G+C content. The phylogenetic analysis suggested that DEV was evolutionarily closer to Alphaherpesvirinae, there was no significant deviation in codon usage in different virus strains. There were 17 codons showing distinct usage differences between DEV and Escherichia coli, 22 between DEV and Homo sapiens but only 15 codons between DEV and yeast. Therefore, the yeast expression system may be more suitable for the expression of DEV genes. The results are encouraging regarding bioinformatics data of an economically important poultry pathogen and could be highly useful for development of new generation vaccines, diagnostics and studying the evolution of the duck enteritis virus. © 2014 Academic Journals Inc.