Analysis of Synonymous Codon Usage in the Capsid Gene UL38 of Duck Enteritis Virus

In the study, we calculated the codon usage bias in the newly identified UL38 gene of Duck Enteritis Virus (DEV) and performed a correlation analysis of codon bias of DEV UL38 gene and its host animal. There was a strong bias in the DEV UL38 gene towards the synonymous codons with A and T at the third codon position. The amino acids codon usage bias in the DEV UL38 gene was compared with other 15 reference herpesviruses, and the cluster analysis suggested that UL38 gene´s type and function also contributed to the codon usage of it. In addition, there were 42 rare condons in the ORF of the DEV UL38, and 24 codons showing distinct usage differences between DEV and E. coli, 12 codons between DEV and Homo sapiens, 25 codons between DEV and yeast.