Analysis of the codon use frequency of AMPK family genes from different species

In mammals, AMP-activated protein kinase (AMPK) is involved in the regulation of cellular energy homeostasis and, on the whole animal level, in regulating energy balance and food intake. In this paper, the relative synonymous codon use frequency of 40 AMPK family genes from seven mammal species (Bos taurus, Homo sapiens, Macaca mulatta, Mus musculus, Pan troglodytes, Rattus norvegicus, Sus scrofa) were analyzed using correspondence analysis and hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias in AMPK family genes, while species is a minor factor that determines further difference in codon usage bias for genes with similar functions.