Characterization of synonymous codon usage bias in pseudorabies virus EP0 gene

Codon usage bias among synonymous codons is not an uncommon phenomenon and it is known to involve various biological factors, such as GC compositions, gene length, mutation frequency and patterns, gene expression level, etc. Knowledge on synonymous codon usage may help in understanding the molecular evolution of the individual gene better. In the present study, we examined the codon usage bias between pseudorabies virus (PRV) EP0 gene and the EP0-like genes of 24 reference alpha herpesviruses. Comparative analysis showed noticeable disparities of the synonymous codon usage bias in the 25 alpha herpesviruses, indicated by codon adaptation index, an effective number of codons (ENc) and GC3s value. The codon usage pattern of PRV EP0 gene was phylogenetically conserved and similar to that of the EP0-like genes of the genus Mardivirus of alphaherpesvirus, with a strong bias towards the codons with C and G at the third codon position. Cluster analysis of codon usage pattern of PRV EP0 gene with its reference alpha herpesviruses demonstrated that the codon usage bias of EP0-like genes of 25 alpha herpesviruses had close relation with their gene functions. ENc-plot revealed that the genetic heterogeneity in PRV EP0 gene and the 24 reference alpha herpesviruses was constrained by G+C content, but not gene length. In addition, comparison of codon preferences in the EP0 gene of PRV with those of E. coli, yeast and human revealed that there were 40 codons showing distinct usage differences between PRV and yeast, 27 between PRV and E. coli, but only 22 between PRV and human. Therefore, the human expression system may be more suitable for expression of PRV EP0 gene. In conclusion, these results may improve our understanding of the evolution, pathogenesis and functional studies of PRV.