Factors affecting synonymous codon usage bias in the gC gene of DPV CHv strain


Fu Xiao Shen1, An Chun Cheng1,2,3*, Ming Shu Wang1,2, Hai Bin Huang1, Chuan Feng Li1,Jin Feng Jiang1, Ren Yong Jia2, De Kang Zhu1,2and Xiao Yue Chen3

The aim was to identify the factors affecting synonymous codon usage bias in the newly discovered gC gene of duck plague virus (DPV) CHv strain and a comparative analysis of the codon usage bias in the gC genes of 27 other reference herpesviruses was performed by using CAI, CHIPS and CUSP program of EMBOSS. The results showed that base composition, mutational bias and natural selection were the major determinants of the codon usage variation in the DPV gC gene. The primary codon usage trends in the DPV gC gene showed obvious difference with a strong bias towards the synonymous codons with A and T at the third codon position. Characterization of nucleotide composition in the DPV gC gene was related to dinucleotide usage bias characterized by the variation of CpG islands. The ENc-plot and GC12s-GC3s revealed that the genetic heterogeneity in the gC genes of the 28 herpesviruses were constrained by G + C content. Moreover, the phylogenetic analysis demonstrated that codon usage patterns of the DPV gC gene were phylogenetically conserved and similar to the gC genes of the avian alphaherpesvirinae. Furthermore, comparisons of the codon preferences in the DPV gC gene with those of Escherichia coli, yeast and human revealed that there was a statistically positive correlation between DPV and yeast (r = 0.646, P < 0.05) . The above results could provide useful information for the synonymous codons usage bias of the DPV gC gene and promote the relevant mechanism for evolution, pathogenesis and functional studies in the area of DPV research and possibly studies with other herpesvirus viruses.

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