Negative Correlation of G+C Content at Silent Substitution Sites Between Orthologous Human and Mouse Protein-Coding Sequences

We conducted a genome-wide analysis of variations in guanine plus cytosine (GþC) content at the third codon position at silent substitution sites of orthologous human and mouse protein-coding nucleotide sequences. Alignments of 3776 human protein-coding DNA sequences with mouse orthologs having >50 synonymous codons were analyzed, and nucleotide substitutions were counted by comparing sequences in the alignments extracted from gap-free regions. The GþC content at silent sites in these pairs of genes showed a strong negative correlation (r ¼� 0.93). Some gene pairs showed significant differences in GþC content at the third codon position at silent substitution sites. For example, human thymine-DNA glycosylase was AþT-rich at the silent substitution sites, while the orthologous mouse sequence was GþCrich at the corresponding sites. In contrast, human matrix metalloproteinase 23B was GþC-rich at silent substitution sites, while the mouse ortholog was AþT-rich. We discuss possible implications of this significant negative correlation of GþC content at silent sites.