Characterization of codon usage bias in the dUTPase gene of duck enteritis virus

Abstract

A comparative analysis of the codon usage bias in the newly discovered dUTPase gene (Assigned Accession No.: DQ486149) of the duck enteritis virus (DEV) and the dUTPase gene of 32 reference herpesviruses was performed. The results indicated that the DEV dUTPase gene encodes a protein of 477 amino acids, which includes five conserved motifs with a 3–1–2–4–5 arrangement. The codon adaptation index (CAI), effective number of codons (ENC), and GC3S values indicated synonymous codon usage bias in the dUTPase gene of herpesviruses, and this synonymous bias was correlated with host evolution. The codon usage patterns of the DEV dUTPase gene were phylogenetically conserved and similar to that of the dUTPase 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, with a strong bias towards A and T at the third codon position, were used. Comparison of the codon usage in the dUTPase gene of different organisms revealed that there were 19 codons showing distinct codon usage differences between the DEV and Escherichia coli dUTPase genes; 16 between the DEV and yeast dUTPase genes; and 15 between the DEV and human dUTPase genes. Analysis of variance (ANOVA) showed significant differences between the DEV and yeast dUTPase genes (r = 0.536, P < 0.01). The extent of codon usage bias in the DEV dUTPase gene was highly correlated with the gene expression level, therefore the results may provide useful information for gene classification and functional studies.