Characterization of Synonymous Codon Usage Bias in the UL19 Gene of Duck Plague Virus (DPV)

Abstract

The codon usage bias of DPV UL19 gene and 25 reference herpesviruses have been analyzed in this study. This work was performed by program CodonW 1.4, and CUSP and CHIPS of EMBOSS. The results indicated that codons of DPV UL19 gene were strong bias towards the synonymous codons with A or T at the third codon position. The codon adaptation index (CAI), effective number of codons (ENC), and GC3s values indicated synonymous codon usage bias in the UL19 gene of herpesviruses, and this synonymous bias was correlated with host evolution. The plot of ENC against GC3s revealed that factors other than gene composition might contribute to the codon usage among the different herpesviruses. The codon usage bias of DPV UL19 gene was compared with that of E. coli, yeast, and Homo sapiens, which might help us understand the relevant mechanism for biased usage of synonymous codons and select appropriate expression systems to improve the expression of target genes. There were 13 codons showing distinct usage differences between DPV and E. coli; 14, between DPV and yeast; and 25, between DPV and Human. We assumed that the DPV UL19 gene might express more efficiently in the E. coli system, yeast as well.