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Selective pressure on synonymous codon usage in mammalian protein‐encoding genes
Author(s) -
ZHANG XinBo,
MA XiangMing,
WANG BaiYun,
MA XiangHui,
WANG ZhiWen
Publication year - 2015
Publication title -
journal of systematics and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.249
H-Index - 46
eISSN - 1759-6831
pISSN - 1674-4918
DOI - 10.1111/jse.12127
Subject(s) - gene , biology , synonymous substitution , genetics , codon usage bias , homo sapiens , genome , molecular evolution , negative selection , selection (genetic algorithm) , evolutionary biology , sociology , anthropology , artificial intelligence , computer science
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.