Analysis of Synonymous Codon Usage in the UL26.5 Gene of Duck Enteritis Virus

Abstract

The analysis on codon usage bias of UL26.5 gene of duck enteritis virus (DEV) may provide a basis for understanding the evolution and pathogenesis of DEV 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 UL26.5 gene of DEV and 27 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 UL26.5 gene of DEV. G + C compositional constraint is the main factor that determines the codon usage bias in UL26.5 gene. The phylogentic analysis suggested that DEV was evolutionarily closer to fowl herpesviruses which further clustered into Alphaherpesvirinae. There were both 21 codons showing distinct usage differences between DEV with Escherichia coli and yeast, 25 between DEV and Homo sapiens, 26 between DEV and adenovirus. Therefore the yeast and E. coli expression system may be suitable for the expression of DEV UL26.5 gene if some codons could be optimized.