Hydrophobicity and Aromaticity Are Primary Factors Shaping Variation in Amino Acid Usage of Chicken Proteome

文献类型： 外文期刊

第一作者： Rao, Yousheng

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

作者机构：

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2014 年 9 卷 10 期

页码：

收录情况： SCI

摘要： Amino acids are utilized with different frequencies both among species and among genes within the same genome. Up to date, no study on the amino acid usage pattern of chicken has been performed. In the present study, we carried out a systematic examination of the amino acid usage in the chicken proteome. Our data indicated that the relative amino acid usage is positively correlated with the tRNA gene copy number. GC contents, including GC1, GC2, GC3, GC content of CDS and GC content of the introns, were correlated with the most of the amino acid usage, especially for GC rich and GC poor amino acids, however, multiple linear regression analyses indicated that only approximately 10-40% variation of amino acid usage can be explained by GC content for GC rich and GC poor amino acids. For other intermediate GC content amino acids, only approximately 10% variation can be explained. Correspondence analyses demonstrated that the main factors responsible for the variation of amino acid usage in chicken are hydrophobicity, aromaticity and genomic GC content. Gene expression level also influenced the amino acid usage significantly. We argued that the amino acid usage of chicken proteome likely reflects a balance or near balance between the action of selection, mutation, and genetic drift.

分类号：

  • 相关文献
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