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 Wang4–6† , Xiang‐Hui Ma4–6 , and Zhi‐Wen Wang4–6*   

  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 Accepted:2014-08-29 Online:2014-10-28 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