Characterization of Codon Usage Bias in UL21gene from Duck Enteritis Virus

Abstract

In this paper, the comprehensive analysis of codon usage bias of Duck enteritis virus (DEV) UL21 gene was performed by using CAI, CHIPS and CUSP program of EMBOSS. Our study showed that codon usage bias of DEV UL21 had strong bias towards the A-ended or T-ended codons, and GC3s contents of the codon usage bias in DEV UL21 gene were significantly varied compared with those of other 27 reference herpesviruses. The CAI, ENC value of DEV CHv strain UL21 gene is 0.615 and 55.167, respectively, indicating that the codon usage bias of this gene is weak and lowly expressed. The plot of ENC versus GC3S content revealed that DEV UL21 gene is subject to GC compositional constraints. The phylogentic analysis about amino acids codon usage bias of DEV UL21 and the27 reference herpesviruses showed that DEV was evolutionarily closer to herpesviruses Mardivirus. In addition, the codon usage bias of DEV UL21 gene was compared with those of E. coli, yeast and humans. There are 42, 45, 39 same codons usage bias between the DEV UL21 to E.coli, Yeast, H.sapiens, respectively, indicaiting that UL21 gene of DEV may be more efficiently expressed in the yeast system.