Non-uniqueness of factors constraint on the codon usage in Bombyx mori

文献类型： 外文期刊

第一作者： Jia, Xian

作者： Jia, Xian;Zheng, Hao;Qi, Qi;Wei, Lei;Sun, Jingchen;Jia, Xian;Zheng, Hao;Qi, Qi;Wei, Lei;Sun, Jingchen;Liu, Shuyu;He, Jian;Li, Bo;Zhao, Taiyi

作者机构：

关键词： Bombyx mori;Codon usage bias;Natural selection;Codon optimization

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2015 年 16 卷

页码：

收录情况： SCI

摘要： Background: The analysis of codon usage is a good way to understand the genetic and evolutionary characteristics of an organism. However, there are only a few reports related with the codon usage of the domesticated silkworm, Bombyx mori (B. mori). Hence, the codon usage of B. mori was analyzed here to reveal the constraint factors and it could be helpful to improve the bioreactor based on B. mori. Results: A total of 1,097 annotated mRNA sequences from B. mori were analyzed, revealing there is only a weak codon bias. It also shows that the gene expression level is related to the GC content, and the amino acids with higher general average hydropathicity (GRAVY) and aromaticity (Aromo). And the genes on the primary axis are strongly positively correlated with the GC content, and GC3s. Meanwhile, the effective number of codons (ENc) is strongly correlated with codon adaptation index (CAI), gene length, and Aromo values. However, the ENc values are correlated with the second axis, which indicates that the codon usage in B. mori is affected by not only mutation pressure and natural selection, but also nucleotide composition and the gene expression level. It is also associated with Aromo values, and gene length. Additionally, B. mori has a greater relative discrepancy in codon preferences with Drosophila melanogaster (D. melanogaster) or Saccharomyces cerevisiae (S. cerevisiae) than with Arabidopsis thaliana (A. thaliana), Escherichia coli (E. coli), or Caenorhabditis elegans (C. elegans). Conclusions: The codon usage bias in B. mori is relatively weak, and many influence factors are found here, such as nucleotide composition, mutation pressure, natural selection, and expression level. Additionally, it is also associated with Aromo values, and gene length. Among them, natural selection might play a major role. Moreover, the "optimal codons" of B. mori are all encoded by G and C, which provides useful information for enhancing the gene expression in B. mori through codon optimization.

分类号：

  • 相关文献

[1]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.

[2]Characterization of the porcine epidemic diarrhea virus codon usage bias. Chen, Ye,Shi, Yuzhen,Deng, Hongjuan,Gu, Ting,Xu, Jian,Ou, Jinxin,Jiang, Zhiguo,Jiao, Yiren,Zou, Tan,Wang, Chong.

[3]SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors. Chen, Liang,Sun, Daokun,Peng, Junhua,Ren, Jing,You, Frank M.,Wang, Jirui,Luo, Ming-Cheng,You, Frank M.,Peng, Yunliang,Nevo, Eviatar,Beiles, Avigdor,Sun, Dongfa,Peng, Junhua. 2013

[4]Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing. Li, Yan,Otecko, Newton O.,Liu, He-Qun,Wang, Ming-Shan,Irwin, David M.,Peng, Ming-Sheng,Wu, Dong-Dong,Zhang, Ya-Ping,Zeng, Lin,Su, Ling-Yan,Otecko, Newton O.,Liu, He-Qun,Wang, Ming-Shan,Peng, Ming-Sheng,Wu, Dong-Dong,Zhang, Ya-Ping,Ming, Chen,Li, Hai-Peng,Ming, Chen,Li, Yan,Zhang, Ya-Ping,Li, Yan,Yao, Yong-Gang,Su, Yan-Hua,Otecko, Newton O.,Peng, Ming-Sheng,Wu, Dong-Dong,Dalecky, Ambroise,Dalecky, Ambroise,Aplin, Ken,Donnellan, Stephen,Aplin, Ken,Liu, Xiao-Hui,Song, Ying,Zhang, Zhi-Bin,Esmailizadeh, Ali,Sohrabi, Saeed S.,Nanaei, Hojjat Asadollahpour,Atteynine, Solimane Ag,Atteynine, Solimane Ag,Rocamora, Gerard,Brescia, Fabrice,Morand, Serge,Irwin, David M.. 2018

[5]Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax. Li, Kexin,Wang, Huihua,Li, Kexin,Zhao, Yang,Frenkel, Zeev,Beiles, Avigdor,Nevo, Eviatar,Wang, Liuyang,Levanon, Erez Y.,Bazak, Lily,Buchumenski, Ilana,Xu, Qinqin,Frenkel-Morgenstern, Milana,Tagore, Satabdi,Fang, Xiaodong,Lovy, Matej,Li, Xiangfeng,Bin Cao, Yi,Wang, Zhen Long.

[6]Sympatric speciation of spiny mice, Acomys, unfolded transcriptomically at Evolution Canyon, Israel. Li, Kexin,Wang, Huihua,Li, Kexin,Lovy, Matej,Nevo, Eviatar,Cai, Zhenyuan,Wang, Liuyang,Xu, Qinqin,Lovy, Matej,Wang, Zhenlong.

[7]Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: An endangered long-lived tree endemic to Hainan Island, China. Zheng, D. -J.,Xie, L. -S.,Zhang, Z. -L.,Zheng, D. -J.,Zhu, J. -H.,Zhang, Z. -L..

[8]Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae). Song, H.,Wang, P. F.,Li, T. T.,Xia, H.,Zhao, S. Z.,Hou, L.,Zhao, C. Z.. 2015

[9]Global Analysis of WRKY Genes and Their Response to Dehydration and Salt Stress in Soybean. Song, Hui,Wang, Pengfei,Hou, Lei,Zhao, Shuzhen,Zhao, Chuanzhi,Xia, Han,Li, Pengcheng,Zhang, Ye,Bian, Xiaotong,Wang, Xingjun. 2016

[10]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

[11]Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes. Chen, L.,Yang, D. Y.,Nong, X.,Huang, X.,Xie, Y.,Fu, Y.,Zheng, W. P.,Zhang, R. H.,Wu, X. H.,Gu, X. B.,Wang, S. X.,Yang, G. Y.,Liu, T. F.,Peng, X. R.. 2013

[12]High-level expression of the Penicillium notatum glucose oxidase gene in Pichia pastoris using codon optimization. Gao, Zhaowei,Zhang, Yuhong,Li, Mu,Zhou, Liwei,Zhang, Wei,Gao, Zhaowei,Tang, Yunming,Li, Zhuofu,Huang, Huoqing,Yao, Bin. 2012

[13]Improved secretory production of calf prochymosin by codon optimization and disruption of PMR1 in Kluyveromyces lactis GG799. Feng, Zhen,Ren, Jing,Zhang, Yanhe,Hu, Sen. 2011

[14]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

[15]Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome. Ma, Yan-Ping,Li, Yu-Gu,Ma, Yan-Ping,Ke, Hao,Liang, Zhi-Ling,Liu, Zhen-Xing,Hao, Le,Ma, Jiang-Yao. 2016

[16]Codon optimization of Bacillus licheniformis beta-1,3-1,4-glucanase gene and its expression in Pichia pastoris. Teng, Da,Fan, Ying,Yang, Ya-lin,Tian, Zi-gang,Luo, Jin,Wang, Jian-hua.

[17]Genetic analysis of the PB1-F2 gene of equine influenza virus. Lu, Gang,Guo, Wei,Qi, Ting,Ma, Jian,Zhao, Shihua,Tian, Zhige,Pan, Jialiang,Zhu, Chao,Wang, Xiaojun,Xiang, Wenhua.

[18]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.

[19]Formation of virus-like particles from O-type foot-and-mouth disease virus in insect cells using codon-optimized synthetic genes. Cao, Yimei,Sun, Pu,Fu, Yuanfang,Bai, Xingwen,Tian, Feipen,Liu, Xiangtao,Lu, Zengjun,Liu, Zaixin.

[20]Characteristics of codon usage bias in two regions downstream of the initiation codons of foot-and-mouth disease virus. Zhou, Jian-hua,Zhang, Jie,Ding, Yao-zhong,Chen, Hao-tai,Ma, Li-na,Liu, Yong-sheng.

作者其他论文 更多>>

微信小程序