A comparative analysis on the synonymous codon usage pattern in viral functional genes and their translational initiation region of ASFV

文献类型： 外文期刊

第一作者： Zhou, Jian-hua

作者： Zhou, Jian-hua;Gao, Zong-liang;Sun, Dong-jie;Ding, Yao-zhong;Zhang, Jie;Liu, Yong-sheng;Stipkovits, Laszlo;Szathmary, Susan;Pejsak, Zygmunt

作者机构：

关键词： African swine fever virus;Synonymous codon usage;Mutation pressure;Translation selection;Translational initiation region

期刊名称：VIRUS GENES （ 影响因子：2.332； 五年影响因子：2.0 ）

ISSN： 0920-8569

年卷期： 2013 年 46 卷 2 期

页码：

收录情况： SCI

摘要： The synonymous codon usage pattern of African swine fever virus (ASFV), the similarity degree of the synonymous codon usage between this virus and some organisms and the synonymous codon usage bias for the translation initiation region of viral functional genes in the whole genome of ASFV have been investigated by some simply statistical analyses. Although both GC(12)% (the GC content at the first and second codon positions) and GC(3)% (the GC content at the third codon position) of viral functional genes have a large fluctuation, the significant correlations between GC(12) and GC(3)% and between GC(3)% and the first principal axis of principle component analysis on the relative synonymous codon usage of the viral functional genes imply that mutation pressure of ASFV plays an important role in the synonymous codon usage pattern. Turning to the synonymous codon usage of this virus, the codons with U/A end predominate in the synonymous codon family for the same amino acid and a weak codon usage bias in both leading and lagging strands suggests that strand compositional asymmetry does not take part in the formation of codon usage in ASFV. The interaction between the absolute codon usage bias and GC(3)% suggests that other selections take part in the formation of codon usage, except for the mutation pressure. It is noted that the similarity degree of codon usage between ASFV and soft tick is higher than that between the virus and the pig, suggesting that the soft tick plays a more important role than the pig in the codon usage pattern of ASFV. The translational initiation region of the viral functional genes generally have a strong tendency to select some synonymous codons with low GC content, suggesting that the synonymous codon usage bias caused by translation selection from the host takes part in modulating the translation initiation efficiency of ASFV functional genes.

分类号：

  • 相关文献

[1]The analysis of codon bias of foot-and-mouth disease virus and the adaptation of this virus to the hosts. Zhou, Jian-hua,Gao, Zong-liang,Zhang, Jie,Ding, Yao-zhong,Liu, Yong-sheng,Stipkovits, Laszlo,Szathmary, Susan,Pejsak, Zygmunt. 2013

[2]Analysis of synonymous codon usage in foot-and-mouth disease virus. Zhou, Jian-Hua,Zhang, Jie,Chen, Hao-Tai,Ma, Li-Na,Liu, Yong-Sheng.

[3]Codon Usage Bias and Determining Forces in Taenia solium Genome. Yang, Xing,Luo, Xuenong,Ling, Houjun,Zhang, Xichen,Cai, Xuepeng,Yang, Xing,Ma, Xusheng,Cai, Xuepeng. 2015

[4]Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome. Su, Jun-hong,Li, Ji-dong,Ma, Xu-sheng,Dou, Yong-xi,Luo, Xue-nong,Cai, Xue-peng,Ma, Xiao-xia,He, Ya-li,Li, Ji-dong. 2011

[5]Pre-Clinical Evaluation of a Real-Time PCR Assay on a Portable Instrument as a Possible Field Diagnostic Tool: Experiences from the Testing of Clinical Samples for African and Classical Swine Fever Viruses. Liu, L.,Stahl, K.,Belak, S.,Liu, L.,Stahl, K.,Belak, S.,Liu, L.,Luo, Y.,Qiu, H. -J.,Luo, Y.,Qiu, H. -J.,Accensi, F.,Ganges, L.,Rodriguez, F.,Accensi, F.,Rodriguez, F.,Shan, H.,Belak, S..

[6]Recombinant Newcastle disease virus expressing African swine fever virus protein 72 is safe and immunogenic in mice. Chen, Xinxin,Yang, Jifei,Ji, Yanhong,Liu, Bin,Li, Xiaoyang,Yin, Hong,Zhu, Qiyun,Yin, Hong,Okoth, Edward. 2016

[7]Roles of African swine fever virus structural proteins in viral infection. Jia, Ning,Ou, Yunwen,Ou, Yunwen,Zhang, Yongguang,Zhang, Jie,Pejsak, Zygmunt. 2017

[8]Comparative the codon usage between the three main viruses in pestivirus genus and their natural susceptible livestock. Zhou, Jian-hua,Gao, Zong-liang,Zhang, Jie,Chen, Hao-tai,Ma, Li-na,Ding, Yao-zhong,Liu, Yong-sheng,Pejsak, Zygmunt. 2012

[9]Analysis of Synonymous Codon Usage in Dengue Viruses. Ma, Jun-Jun,Zhao, Feng,Zhang, Jie,Zhou, Jian-Hua,Ma, Li-Na,Ding, Yao-Zhong,Chen, Hao-Tai,Gu, Yuan-Xing,Liu, Yong-Sheng.

[10]The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern. Liu, Yong-sheng,Zhou, Jian-hua,Chen, Hao-tai,Ma, Li-na,Ding, Yao-zhong,Zhang, Jie,Pejsak, Zygmunt.

[11]Analysis of codon usage in peste des petits ruminant's virus. Liu, Xin-sheng,Wang, Yong-lu,Zhang, Yong-guang,Fang, Yu-zhen,Pan, Li,Lu, Jian-liang,Zhou, Peng,Zhang, Zhong-wang,Jiang, Shou-tian. 2011

[12]Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus. Wang, Meng,Zhang, Jie,Zhou, Jian-hua,Chen, Hao-tai,Ma, Li-na,Ding, Yao-zhong,Liu, Wen-qian,Gu, Yuan-xing,Zhao, Feng,Liu, Yong-sheng. 2011

[13]Effects of nucleotide usage on the synonymous codon usage patterns of biofilm-associated genes in Haemophilus parasuis. Wang, L. Y.,Ma, L. N.,Liu, Y. S.. 2016

[14]The effects of the synonymous codon usage and tRNA abundance on protein folding of the 3C protease of foot-and-mouth disease virus. Zhou, Jian-hua,You, Ya-nan,Chen, Hao-tai,Zhang, Jie,Ma, Li-na,Ding, Yao-zhong,Liu, Yong-sheng,Pejsak, Zygmunt.

[15]Chemical gene synthesis: strategies, softwares, error corrections, and applications. Xiong, Ai-Sheng,Peng, Ri-He,Zhuang, Jing,Gao, Feng,Yao, Quan-Hong,Cheng, Zong-Ming,Li, Yi.

[16]Analysis of codon usage in Newcastle disease virus. Wang, Meng,Liu, Yong-sheng,Zhou, Jian-hua,Chen, Hao-tai,Ma, Li-na,Ding, Yao-zhong,Liu, Wen-qian,Gu, Yuan-xing,Zhang, Jie. 2011

作者其他论文 更多>>

微信小程序