Mutation Bias is the Driving Force of Codon Usage in the Gallus gallus genome

文献类型： 外文期刊

第一作者： Rao, Yousheng

作者： Rao, Yousheng;Wu, Guozuo;Wang, Zhangfeng;Chai, Xuewen;Rao, Yousheng;Nie, Qinghua;Zhang, Xiquan;Nie, Qinghua;Zhang, Xiquan

作者机构：

关键词： Gallus gallus;codon usage;mutation;selection

期刊名称：DNA RESEARCH （ 影响因子：4.458； 五年影响因子：5.371 ）

ISSN： 1340-2838

年卷期： 2011 年 18 卷 6 期

页码：

收录情况： SCI

摘要： Synonymous codons are used with different frequencies both among species and among genes within the same genome and are controlled by neutral processes (such as mutation and drift) as well as by selection. Up to now, a systematic examination of the codon usage for the chicken genome has not been performed. Here, we carried out a whole genome analysis of the chicken genome by the use of the relative synonymous codon usage (RSCU) method and identified 11 putative optimal codons, all of them ending with uracil (U), which is significantly departing from the pattern observed in other eukaryotes. Optimal codons in the chicken genome are most likely the ones corresponding to highly expressed transfer RNA (tRNAs) or tRNA gene copy numbers in the cell. Codon bias, measured as the frequency of optimal codons (Fop), is negatively correlated with the G + C content, recombination rate, but positively correlated with gene expression, protein length, gene length and intron length. The positive correlation between codon bias and protein, gene and intron length is quite different from other multi-cellular organism, as this trend has been only found in unicellular organisms. Our data displayed that regional G 1 C content explains a large proportion of the variance of codon bias in chicken. Stepwise selection model analyses indicate that G + C content of coding sequence is the most important factor for codon bias. It appears that variation in the G + C content of CDSs accounts for over 60% of the variation of codon bias. This study suggests that both mutation bias and selection contribute to codon bias. However, mutation bias is the driving force of the codon usage in the Gallus gallus genome. Our data also provide evidence that the negative correlation between codon bias and recombination rates in G. gallus is determined mostly by recombination-dependent mutational patterns.

分类号：

  • 相关文献

[1]Relationship between 5 ' UTR length and gene expression pattern in chicken. Rao, You S.,Wang, Zhang F.,Chai, Xue W.,Rao, You S.,Nie, Qing H.,Zhang, Xi Q..

[2]Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rational engineering of a glycine to proline mutation. Tian, Jian,Wang, Ping,Gao, Shan,Chu, Xiaoyu,Wu, Ningfeng,Fan, Yunliu.

[3]Generation and characterization of low phytic acid germplasm in rice (Oryza sativa L.). Liu, Qing-Long,Xu, Xiu-Hong,Ren, Xue-Liang,Fu, Hao-Wei,Wu, Dian-Xing,Shu, Qing-Yao.

[4]Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Mwacharo, J. M.,Hanotte, O.,Bjornstad, G.,Bjornstad, G.,Mobegi, V.,Jianlin, H.,Hanotte, O.,Nomura, K.,Hanada, H.,Jianlin, H..

[5]Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Gongora, Jaime,Moran, Chris,Rawlence, Nicolas J.,Cooper, Alan,Mobegi, Victor A.,Jianlin, Han,Hanotte, Olivier,Jianlin, Han,Alcalde, Jose A.,Matus, Jose T.,Ulm, Sean,Larson, Greger,Larson, Greger,Anderson, Atholl J..

[6]Reconstructing the origin and dispersal patterns of village chickens across East Africa: Insights from autosomal markers. Mwacharo, J. M.,Hanotte, O.,Nomura, K.,Hanada, H.,Amano, T.,Han, J. L.,Han, J. L..

[7]Synonymous codon usage and gene function are strongly related in Oryza sativa. Liu, QP,Dou, SJ,Ji, ZJ,Xue, QZ. 2005

[8]Analysis of codon usage in Lilium longiflorum Thunb.. Xu, L. F.,Feng, H. Y.,Liang, Y.,Yuan, S. X.,Liu, C.,Ming, J..

[9]The characteristic of codon usage pattern and its evolution of hepatitis C virus. Hu, Jin-song,Wang, Qin-qin,Zhang, Jie,Chen, Hao-tai,Ding, Yao-zhong,Ma, Li-na,Gu, Yuan-xing,Liu, Yong-sheng,Hu, Jin-song,Xu, Zhi-wen,Zhu, Ling,Xu, Kai.

[10]Bioinformatics analysis of rabbit haemorrhagic disease virus genome. Tian, Xiao-ting,Li, Bao-yu,Zhang, Liang,Jiao, Wen-qiang,Liu, Ji-xing. 2011

[11]A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences. Xiong, Ai-Sheng,Peng, Ri-He,Zhuang, Jing,Liu, Jin-Ge,Gao, Feng,Xu, Fang,Cai, Bin,Yao, Quan-Hong.

[12]Comparative analysis of codon usage and tRNA in mitochondrial genomes of Gallus gallus. Zhang, Tangjie,Chang, Hong,Liu, Yuzhi,Li, Huifang,Chen, Kuanwei. 2009

[13]Genetic effects on flight capacity in the beet armyworm, Spodoptera exigua (Lep., Noctuidae). Zhai, B. P.,Zhang, X. X.,Han, L. Z.,Gu, H. N.. 2009

[14]Cloning and sequence diversity analysis of GmHs1(pro-1) in Chinese domesticated and wild soybeans. Yuan, Cuiping,Zhou, Guoan,Li, Yinghui,Wang, Kejing,Li, Xianghua,Chang, Ruzhen,Qiu, Lijuan,Wang, Zhi. 2008

[15]Genotype x environment interactions in sugarcane between China and Australia. Jackson, Phillip,Chen, Xuekuan,Fan, Yuanhong,Liu, Jiayong,Shen, Wankuan,Deng, Haihua,Li, Qiwei,Hu, Fengduo. 2012

[16]Polymorphic microsatellite differences among four cultured populations of two selected tilapia strains. Li, Dayu,Yang, Hong,Zou, Zhiying,Xiao, Wei,Zhu, Jingling,Luo, Yongju.

[17]Selection of housekeeping genes for gene expression studies on the development of fruit bearing shoots in Chinese jujube (Ziziphus jujube Mill.). Sun, Hai-feng,Meng, Yu-ping,Cui, Gui-mei,Cao, Qiu-fen,Sun, Hai-feng,Liang, Ai-hua,Sun, Hai-feng,Li, Jie.

[18]Application of identified QTL-marker associations in rice quality improvement through a design-breeding approach. Wang, Jiankang,Wan, Xiangyuan,Li, Huihui,Pfeiffer, Wolfgang H.,Crouch, Jonathan,Wan, Jianmin.

[19]A non-destructive method to predict polyphenol content in strawberry. Fan, Li,Dube, Claudine,Tremblay, Nicolas,Khanizadeh, Shahrokh,Fan, Li,Fang, Chengquan.

[20]Detecting SNPs underlying domestication-related traits in soybean. Li, Ying-Hui,Ma, Yan-Song,Chang, Ru-Zhen,Qiu, Li-Juan,Reif, Jochen C.,Jackson, Scott A.,Ma, Yan-Song. 2014

作者其他论文 更多>>
  • The transmembrane protein TMEM182 promotes fat deposition and alters metabolomics and lipidomics

    作者：Chen, Genghua;Lin, Zetong;Peng, Haoqi;Zhang, Shuai;Zhang, Zihao;Zhang, Xiquan;Nie, Qinghua;Luo, Wen;Chen, Genghua;Lin, Zetong;Peng, Haoqi;Zhang, Shuai;Zhang, Zihao;Zhang, Xiquan;Nie, Qinghua;Chen, Genghua;Lin, Zetong;Peng, Haoqi;Zhang, Shuai;Zhang, Zihao;Zhang, Xiquan;Nie, Qinghua

    关键词：TMEM182; Fat formation; Metabolomics; Lipidomics

  • Using multiomics to explore the weight differences between genders in Muscovy ducks

    作者：Tian, Jinghong;Tan, Liangtian;Wei, Shenghua;Yao, Zipei;Xu, Yibin;Nie, Qinghua;Tian, Jinghong;Tan, Liangtian;Wei, Shenghua;Yao, Zipei;Xu, Yibin;Nie, Qinghua;Tian, Jinghong;Tan, Liangtian;Wei, Shenghua;Yao, Zipei;Xu, Yibin;Nie, Qinghua;Tian, Jinghong;Tan, Liangtian;Wei, Shenghua;Yao, Zipei;Xu, Yibin;Nie, Qinghua;Zhu, Weijian;Ji, Congliang

    关键词：Muscovy duck; sexual dimorphism; growth and development; RNA-seq; 16S rRNA sequencing technology

  • PMAIP1 promotes J subgroup avian leukosis virus replication by regulating mitochondrial function

    作者：Zhao, Yongxia;Zhao, Changbin;Pan, Ming;Mo, Guodong;Liao, Zhiying;Zhang, Xiquan;Zhang, Dexiang;Li, Hongmei;Zhao, Yongxia;Zhao, Changbin;Deng, Yuelin;Pan, Ming;Mo, Guodong;Liao, Zhiying;Zhang, Xiquan;Zhang, Dexiang;Li, Hongmei;Zhao, Yongxia;Zhao, Changbin;Deng, Yuelin;Pan, Ming;Mo, Guodong;Liao, Zhiying;Zhang, Xiquan;Zhang, Dexiang;Li, Hongmei;Zhao, Yongxia;Zhao, Changbin;Deng, Yuelin;Pan, Ming;Mo, Guodong;Liao, Zhiying;Zhang, Xiquan;Zhang, Dexiang;Li, Hongmei;Deng, Yuelin

    关键词：ALV-J; PMAIP1; mitochondrial function; immune; DF-1

  • Live chicken body fat measurement technology based on bio-electrical impedance

    作者：Liang, Jinping;Li, Zhenhui;Nie, Qinghua;Zhang, Dexiang;Zhang, Xiquan;Li, Hongmei;Zuo, Jiaming;Cheng, Shangshang;Li, Zhen;Zuo, Jiaming;Cheng, Shangshang;Li, Zhen;Liang, Jinping;Li, Zhenhui;Nie, Qinghua;Zhang, Dexiang;Zhang, Xiquan;Li, Hongmei;Liang, Jinping;Li, Zhenhui;Nie, Qinghua;Zhang, Dexiang;Zhang, Xiquan;Li, Hongmei;Liang, Jinping;Li, Zhenhui;Nie, Qinghua;Zhang, Dexiang;Zhang, Xiquan;Li, Hongmei;Deng, Yuelin

    关键词：BIA; Electrical impedance; Fat content; Broilers

  • Whole-transcriptome sequencing revealed the ceRNA regulatory network during the proliferation and differentiation of goose myoblast

    作者：Zhang, Xiquan;Luo, Wen;Zhang, Xiquan;Luo, Wen;Xiao, Liangchao;Chen, Jiahui;He, Xueying;Zhang, Xiquan;Luo, Wen;Xiao, Liangchao;Chen, Jiahui;He, Xueying;Zhang, Xiquan;Luo, Wen;Xiao, Liangchao;Chen, Jiahui;He, Xueying;Zhang, Xiquan;Luo, Wen

    关键词：Shitou goose; skeletal muscle; whole-transcriptome sequencing; lncRNA; ceRNA network

  • LncEDCH1 g.1703613 T>C regulates chicken carcass traits by targeting miR-196-2-3p

    作者：Yuan, Rongshuai;Cai, Bolin;Ma, Manting;Zhao, Changbin;Xian, Yuanrong;Nie, Qinghua;Zhang, Xiquan;Zhang, Dexiang;Zhang, Dexiang

    关键词：LncEDCH1; miR-196-2-3p; single nucleotide polymorphism; carcass trait; chicken

  • Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population

    作者：Pan, Rongyang;Qi, Lin;Xu, Zhenqiang;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen;Pan, Rongyang;Qi, Lin;Xu, Zhenqiang;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen;Pan, Rongyang;Pan, Rongyang;Qi, Lin;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen;Pan, Rongyang;Qi, Lin;Xu, Zhenqiang;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen;Pan, Rongyang;Qi, Lin;Xu, Zhenqiang;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen

    关键词：Chinese yellow-feathered chicken; weighted single-step GWAS; carcass traits; SNP

微信小程序