Codon-pair usage and genome evolution

The aim of this paper is to demonstrate possible evolutionary constraints that shape codon-pair context. The distributions of numbers of modes (DNM) of codon-pairs in protein coding sequences (CDSs) and the frequency of base triplet pairs in intergenic sequences (IGSs) are analyzed in 110 fully sequenced genomes. We propose that these distributions are in accordance with a gamma distribution. By studying the shape parameter α value of gamma distribution a distinct relation between the α value and the genome evolution is obtained. For codon-pairs in CDSs, the α value increases in the order Archaea, Bacteria, and Eukaryota, and divides the species into three evolutionary groups, Archaea, Bacteria and Eukaryota. For triplet pairs in IGSs, on the other hand, the α value classifies the species into two groups, one is Bacteria and the other is Archaea and Eukaryota. The findings suggest that the codon-pair context could be an important determinant for phylogeny of individual species, and indicate the existence of fundamental differences of evolutional constraints imposed on CDSs and IGSs among Archaea, Bacteria, and Eukaryota.