Characterization of Codon Usage Bias in the Newly Identified DPV gE Gene

The Duck Plague Virus (DPV) gE gene was identified by constructing the DPV genomic library, and we analyzed the codon usage of DPV gE gene by using CAI, CHIPS and CUSP program of EMBOSS. The results showed that codon usage bias in the DPV gE gene was strong bias towards the synonymous codons with A and T at the third codon position. The amino acids codon usage bias in the DPV gE gene was compared with other 15 reference herpes viruses, the cluster analysis demonstrated that the codon usage bias of DPV gE gene has a very close relation with its gene function and gene type. In addition, rare condons analysis showed that there are 62 rare condons (33.3%) in the ORF of the DPV gE on line (http//:www.kazusa.or.jp/codon), and the codon usage bias of DPV gE gene was compared with those of E. coli, yeast and Humans. There are 24 codons showing distinct usage differences between DPV and E. coli, 19 between DPV and Homo sapiens, 15 codons between DPV and yeast.