Analysis of synonymous codon usage on the small subunit of ribonucleotide reductase gene from duck plague virus

Duck plague virus (DPV) is a widespread virus in all members of the family Anatidae of the order Anseriformes, and it has been classified into the family Herpesviridae. In this study, the relative synonymous codon usage (RSCU) values, effective number of codons (ENC) values, and the frequencies of nucleotide G + C at the third position (GC3s) contents were investigated, meanwhile, a comparative analysis of codon usage patterns and a phylogenetic analysis for the small subunit of ribonucleotide reductase (R2) gene of DPV and the other 25 herpesviruses were performed. The optimal codons for each amino acid were A-ended or T-ended in the 59 sense codons from the RSCU values of DPV R2 gene. The comparative analysis of the ENC values, and GC3s contents showed the codon usage patterns were not phylogenetically conserved among these 26 herpesvirus R2 genes, but similarity in different genera, and that DPV was close to the mardivirus and the iltovirus. In addition, the plot of ENC vs. GC3s of the 26 herpesvirus R2 genes indicated that the genetic characteristics of R2 gene possibly resulted from mutation pressure. Furthermore, the phylogenetic analysis revealed that DPV may be a part of the alphaherpesvirus, and exhibit a close relationship with the mardivirus and the simplexvirus.