Characterization of Codon Usage Bias in the Us4 Gene of Duck Plague Virus

Abstract

The analysis on codon usage bias of Us4 gene of Duck Plague Virus (DPV) may provide a basis for understanding the evolution and pathogenesis of DPV and for selecting appropriate host expression systems to improve the expression of target genes in vivo and in vitro. In this study, the synonymous codon usage in the Us4 gene of DPV and 17 reference herpesviruses have been investigated . The results reveals that the synonymous codons with A and T at the third codon positon have widely usage in the codon of Us4 gene of DPV. The phylogentic analysis suggested that DPV was evolutionarily closer to fowl herpesviruses which further clustered into Alphaherpesvirinae. In addition, rare condons analysis showed that there are 36 rare condons in the ORF of the DPV Us4 on line (http://nihserver.mbi.ucla.edu/RACC/), and the codon usage bias of DPV Us4 gene was compared with those of E. coli, yeast and Humans. There are 25 codons showing distinct usage differences between DPV and E. coli, 25 codons between DPV and yeast, 27 between DPV and Homo sapiens. Therefore the E. coli and yeast expression system may be suitable for the expression of DPV Us4 gene if some codons could be optimized.