Synonymous Codon Usage Bias in the UL47 Gene of Duck Enteritis Virus

In order to understand the relevant mechanism for biased usage of synonymous codons and the evolution and pathogenesis of DEV better, as well as for selecting appropriate expression systems to improve the expression of the target genes, we performed a comparative analysis of the codon usage bias in the UL47 gene of the duck enteritis virus (DEV) and the 26 reference herpesviruses. The results indicated that the codon usage patterns of the DEV UL47 gene were phylogenetically conserved and similar to that of the UL47 genes of the avian alphaherpesvirus. Although codon usage in each microorganism was different, there were no strain-specific differences among them. Sixty-one codons in the predicted polypeptide were used with a strong bias towards G and C at the third codon position, and the effective number of codons(ENC) used in a gene plot revealed that the genetic heterogeneity in UL47 gene of herpesviruses was constrained by the G + C content. Comparison of the codon usage in the UL47 gene of different organisms revealed that there were 30 codons showing distinct usage differences between DEV and Escherichia coli, equivalently 24 between DEV-to- yeast and DEV-to- human. Therefore, the eukaryotic expression system may be more suitable for the expression of the DEV UL47 gene.