J Syst Evol ›› 2015, Vol. 53 ›› Issue (2): 191-195.doi: 10.1111/jse.12127

• Research Articles • Previous Articles     Next Articles

Selective pressure on synonymous codon usage in mammalian protein-encoding genes

Xin-Bo ZHANG1,2†, Xiang-Ming MA3†, Bai-Yun WANG4,5,6†, Xiang-Hui MA4,5,6 and Zhi-Wen WANG4,5,6*   

  1. 1School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin, China
    2Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin, China
    3Department of Hepatobiliary Surgery, Kailuan General Hospital, Tangshan, Hebei, China
    4Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
    5Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
    6SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
  • Received:2014-02-27 Online:2014-08-29 Published:2015-03-25

Abstract: The evolutionary suppression of synonymous codon sites is a controversial topic. Although some studies have indicated that synonymous substitution is under positive selection, most of these studies relied on comparison of homologous genes and/or a limited number of sequences. In the present work, we compared the selection strength at synonymous sites for two types of protein-encoding genes: genes encoding enzymes and protein genes encoding non-enzymes. Our method does not require assumptions concerning, for example, evolutionary equilibrium or population size. We compared ∼70 000 genes from the fully sequenced mammalian Homo sapiens, Pan troglodytes, Mus musculus, and Rattus norvegicus genomes and found that the percentage of C and G in the third position of a codon positively correlates with the percentage of the G/C content within ± 20 000 nucleotides of the gene. More interestingly, we found that synonymous sites in mammalian genes encoding enzymes have undergone stronger selection than did such sites in genes encoding proteins that are not enzymes.

Key words: codon bias, GC content, mammal, selection, synonymous substitution

[1] Jing-Jing Sun, Tao Zhou, Rui-Ting Zhang, Yun Jia, Yue-Mei Zhao, Jia Yang, and Gui-Fang Zhao. Comparative transcriptomes and development of expressed sequence tag‐simple sequence repeat markers for two closely related oak species . J Syst Evol, 2019, 57(5): 440-450.
[2] Mason W. Kulbaba, Ilona C. Clocher, Lawrence D. Harder. Inflorescence characteristics as function-valued traits: Analysis of heritability and selection on architectural effects . J Syst Evol, 2017, 55(6): 559-565.
[3] Man Zhao, Xiangxian Ying, Jie SunZhao Wang. Molecular evolution of Coq1 gene family in eukaryotes . J Syst Evol, 2017, 55(5): 417-425.
[4] Michael Kessler, Dirk Nikolaus Karger, Jürgen Kluge. Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes . J Syst Evol, 2016, 54(6): 617-625.
[5] Xiao-Ming Zheng, Fu-Qing Wu, Xin Zhang, Qi-Bing Lin, Jie Wang, Xiu-Ping Guo, Cai-Lin Lei, Zhi-Jun Cheng, Cheng Zou, Jian-Min Wan. Evolution of the PEBP gene family and selective signature on FT-like clade . J Syst Evol, 2016, 54(5): 502-510.
[6] Weronika B. Żukowska, Witold Wachowiak. Utility of closely related taxa for genetic studies of adaptive variation and speciation: Current state and perspectives in plants with focus on forest tree species . J Syst Evol, 2016, 54(1): 17-28.
[7] Xiang-Guang MA, Cai ZHAO, Chang-Bao WANG, Qian-Long LIANG,Xing-Jin HE. Phylogenetic analyses and chromosome counts reveal multiple cryptic species in Bupleurum commelynoideum (Apiaceae) . J Syst Evol, 2015, 53(1): 104-116.
[8] Prabodh K. BAJPAI, Ashish R. WARGHAT, Anil KANT, Ravi B. SRIVASTAVA, Tsering STOBDAN. Detecting molecular signatures of natural selection in Morus alba populations from trans-Himalaya . J Syst Evol, 2014, 52(5): 589-597.
[9] Chao YANG, Zhe WANG, Xiao YANG, Bao-Rong LU. Segregation distortion affected by transgenes in early generations of rice crop-weed hybrid progeny: Implications for assessing potential evolutionary impacts from transgene flow into wild relatives . J Syst Evol, 2014, 52(4): 466-476.
[10] Dong-Na LI, Chuan-Chao WANG, Yan LU, Zhen-Dong QIN, Kun YANG, Xue-Jing LIN, Hui LI. Three phases for the early peopling of Hainan Island viewed from mitochondrial DNA . J Syst Evol, 2013, 51(6): 671-680.
[11] Shu-Jun LIU, Xiao-Qiu DU, Feng WU, Xue-Lei LIN, Qi-Jiang XU, Zheng MENG. Evolutionary divergence of the PISTILLATA-like proteins in Hedyosmum orientale (Chloranthaceae) after gene duplication . J Syst Evol, 2013, 51(6): 681-692.
[12] Bao-Hua SONG, Thomas MITCHELL-OLDS. Evolutionary and ecological genomics of non-model plants . J Syst Evol, 2011, 49(1): 17-24.
[13] SHI Jun, CHENG Jin, LUO Dun, SHANGGUAN Fa-Zhi, LUO Yi-Bo. Pollination syndromes predict brood-site deceptive pollination by female hoverflies in Paphiopedilum dianthum (Orchidaceae) . J Syst Evol, 2007, 45(4): 551-560.
Full text



No Suggested Reading articles found!