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Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus

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Abstract

The analysis on codon usage bias of UL24 gene of duck enteritis virus (DEV) may improve our understanding of the evolution and pathogenesis of DEV and provide a basis for understanding the relevant mechanism for biased usage of synonymous codons and for selecting appropriate expression systems to improve the expression of target genes. The codon usage bias of UL24 genes of DEV and 27 reference herpesviruses were analyzed. The results showed that codon of UL24 gene of DEV was strong bias toward the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed, and the effective number of codons used in a gene plot revealed that the genetic heterogeneity in UL24 gene of herpesviruses was constrained by the G + C content. The phylogentic analysis suggested that DEV was evolutionarily closer to Alphaherpesvirinae and that there was no significant deviation in codon usage in different virus strains. There were 20 codons showing distinct usage differences between DEV and Escherichia coli, 23 between DEV and Homo sapiens, but only 16 codons between DEV and yeast. Therefore the yeast expression system may be more suitable for the expression of DEV genes.

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Acknowledgments

The research was supported by the National Natural Science Foundation of China (30771598), New Century Excellent Talents program in University (NCET-06-0818), Scientific and Technological Innovation Major Project Funds in University (706050), National Science and Technology Support Programs (2007Z06-017), the Cultivation Fund of the Key Scientific and Technical Innovation Project, department of Education of Sichuan Province (07ZZ028), Sichuan Province Outstanding Youths Fund (03ZQ026-029/05ZQ026-038/07ZQ026-132), Sichuan Province Research Program (04JY021-100/04JY029-006-1/05JY029-109/05JY029-003/07JY029-016/07ZA051) and Program for Key Disciplines Construction of Sichuan Province (SZD0418).

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Authors and Affiliations

  1. Key Laboratory of Animal Disease and Human Health of Sichuan Province, Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Yaan, 625014, People’s Republic of China

    Renyong Jia, Anchun Cheng, Mingshu Wang, Hongyi Xin, Yufei Guo, Dekang Zhu, Xuefeng Qi, Lichan Zhao, Han Ge & Xiaoyue Chen

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  1. Renyong Jia
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  2. Anchun Cheng
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Correspondence to Anchun Cheng.

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Renyong Jia, Anchun Cheng, Mingshu Wang, and Hongyi Xin contributed equally to this work and should be considered as first author.

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Jia, R., Cheng, A., Wang, M. et al. Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus. Virus Genes 38, 96–103 (2009). https://doi.org/10.1007/s11262-008-0295-0

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