Characterization of codon usage bias in the gI gene of duck enteritis virus

The analysis on codon usage bias of gI gene of duck enteritis virus (DEV) may provide a basis for understanding the evolution and molecular characteristic of DEV, and for selecting appropriate host expression systems to improve the expression of target gene. A comparative analysis of the codon usage bias of the DEV gI gene and 22 other refrence herpesviruses gI-like genes was performed, by using the CAI, CHIPS and CUSP programs of EMBOSS and the CodonW 1.4 program. The results showed that DEV gI gene was strong bias towards the synonymous codons with A and T at the third codon position, and was low codon usage bias gene, presumed lower expression. The ENc-plot revealed that G + C compositional constraint is the main factor that determines the codon usage bias in the herpesvirus gI-like genes. The phylogentic analysis suggested that DEV was evolutionarily closer to avian herpesviruses, condon usage pattern in the 23 herpesviruses gI-like genes was phylogenetically conserved, host species and gene function also had a certain influence to the codon usage bias. There were 26 codons showing distinct usage differences between DEV and Escherichia coli, 24 between DEV and yeast, 31 between DEV and Homo sapiens. Therefore the yeast and E. coli expression system may be suitable for the expression of DEV gI gene if some codons could be optimized.