Characterization of synonymous codon usage bias in the duck plague virus UL35 gene.
OBJECTIVE
The aim was to identify the codon usage bias between the newly identified duck plague virus (DPV) UL35 gene (GenBank accession No. EF643558) and the UL35-like genes of 27 other reference herpesviruses.


METHODS
A comparative analysis of the codon usage bias of the 28 herpesviruses was performed by using the CodonW 1.4 program and CUSP (create a codon usage table) program of EMBOSS (The European Molecular Biology Open Software Suite).


RESULTS
The results showed obvious differences of the synonymous codon usage bias in the 28 herpesviruses indicated by the Codon Adaptation Index, effective number of codons (ENc), and the value of G + C content at the 3rd codon position. The codon usage pattern of the DPV UL35 gene was phylogenetically conserved and similar to that of the UL35-like genes of the avian alpha-herpesvirus, with a strong bias towards the codons with A and T at the 3rd codon position. A cluster analysis of codon usage pattern of the DPV UL35 gene with other reference herpesviruses demonstrated that the codon usage bias of the UL35 genes of the 28 herpesviruses had a very close relation with their gene function. The ENc-plot revealed that the genetic heterogeneity in the DPV UL35 gene and the 27 reference herpesviruses were constrained by G + C content, while gene length exerted relatively weaker influences. In addition, comparisons of the codon preferences in the UL35 gene of DPV with those of Escherichia coli, yeast and humans revealed that there were 33 codons showing distinct usage differences between the DPV and yeast, and 38 between the DPV and humans, but only 31 between the DPV and E. coli. Therefore, the E. coli system may be more suitable for the expression of the DPV UL35 gene.


CONCLUSIONS
Together, these results may improve our understanding of the evolution, pathogenesis and functional studies of DPV, as well as contribute significantly to the area of herpesvirus research and possibly studies with other viruses.
Cai
Ming-Sheng
MS
Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Yaan, China.
Cheng
An-Chun
AC
Wang
Ming-Shu
MS
Zhao
Li-Chan
LC
Zhu
De-Kang
DK
Luo
Qi-Hui
QH
Liu
Fei
F
Chen
Xiao-Yue
XY
D000818:Animals; D036022:Capsid Proteins / Q000235:genetics*; D016000:Cluster Analysis; D003062:Codon; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D004372:Ducks; D019143:Evolution, Molecular; D006564:Herpesviridae / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D014777:Virus Diseases / Q000662:veterinary*
D036022:Capsid Proteins; D003062:Codon; D004279:DNA, Viral