Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification

DNA methylation in CpGs dinucleotides in associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analyzed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF to identify possible correlations with mutations in the domesticated breeds. Our study shows that CpG mutation dynamics differ considerably depending on whether they relate to SNPs or CNVs. While CpG-mutations associated with CNVs would promote genomic 'flexibility', CpG-mutations associated with SNPs would relate to genomic 'specificity' in evolution.