Identification of Synonymous Codon Usage Bias in the Pseudorabies Virus UL31 Gene

Background: Little knowledge of synonymous codon usage pattern of pseudorabies virus (PRV) genome, especially the UL31 gene in the process for its evolution is available. Objectives: In the present study, the codon usage bias between PRV UL31 sequence and the UL31-like sequences was identified. Materials and Methods: We used a comprehensive analysis on codon usage pattern in the PRV UL31 gene and the UL31-like genes of 48 reference herpesviruses by calculating codon adaptation index, ENc, RSCU and EMBOSS assays. Results: Cluster analysis demonstrated that the codon usage bias of UL31-like genes of 49 herpesviruses had a very close relation to their gene functions. In addition, comparison of codon preferences in the UL31 gene of PRV with those of E. coli, yeast and human showed that there were 33 codons showing discrete usage differences between PRV and yeast, 24 between PRV and E. coli, but 22 between PRV and human. Although there were slightly fewer differences in codon usages between PRV and human, the difference is unlikely to be statistically significant, and experimental studies are necessary to establish the most suitable expression system for PRV UL31. Conclusion: These results may further our comprehending of the evolution, pathogenesis and functional studies of PRV.