Background: In contrast to the majority of mammalian genes, imprinted genes are monoallelically expressed with the choice of the active allele depending on its parental origin. Due to their special inheritance patterns, maternally and paternally expressed genes might be under different evolutionary pressure. Here, we aimed at assessing the evolutionary history of imprinted genes.
Results: In this study, we investigated the conservation of imprinted genes in vertebrate genomes and their exposition to natural selection. In a genome-wide comparison, orthologs of imprinted genes show a stronger divergence on cDNA and protein level in mammals. This pattern is most pronounced for maternally expressed genes in rodents in comparison to their non-rodent orthologs. The divergence is not attributable to increased mutation of CpG positions. It is contrasted by strong conservation of paternally expressed genes in mouse and rat. Interestingly, we found that the early divergence of imprinted genes was accompanied by an unusually strict conservation of their paralogs.
Conclusions: The apparent degeneration of maternally expressed genes may reflect a relaxation of selective pressure due to counteracting effects on maternal and embryonic fitness. Functional redundancy provided by the presence of highly conserved (non-imprinted) paralogs may have facilitated the divergence. Moreover, intensification of imprinting in modern rodents seems to have shifted the evolutionary fate of imprinted genes towards strong purifying selection.