Affiliations: 1) Columbia University, New York, NY; 2) University of Cambridge, Cambridge, United Kingdom; 3) University of California, Los Angeles, CA; 4) Stanford University, Stanford, CA; 5) University of Geneva, Geneva, Switzerland
Keywords: Comparative genomics & genome evolution
Comparisons among model organisms make clear that, despite the fundamental importance of recombination in sexually-reproducing species, the mechanisms by which it is directed to the genome can vary markedly. Notably, in mammals such as humans and mice, recombination occurs at the binding sites of the protein PRDM9 and the binding affinity of PRDM9 is rapidly evolving. In other species such as birds or canids, PRDM9 has been lost and recombination occurs preferentially at promoter-like features, such as CpG islands, through unknown mechanisms. Our previous work showed that PRDM9 arose before the origin of vertebrates and is rapidly evolving where the PRDM9 ortholog is intact. This finding led us to postulate that some species outside of mammals also use PRDM9 to direct recombination. To test this prediction, we focused on the corn snake Pantherophis guttatus, a species with a complete PRDM9 ortholog that is rapidly evolving. We improved the assembly and annotation of the reference genome and resequenced 22 unrelated corn snake samples to high coverage in order to infer historical recombination rates across the genome from patterns of linkage disequilibrium. In contrast to what is seen in mammals with PRDM9, we found evidence for elevated recombination around computationally predicted PRDM9 binding sites but also near CpG islands. To verify these findings, we resequenced two families with five offspring, identified the PRDM9 alleles segregating in the families and called crossover events that occurred in the parents. This analysis confirmed that crossover events overlap both PRDM9 binding sites and CpG islands more than expected by chance. These findings indicate that corn snakes behave neither like mammalian species with PRDM9 nor like species that lack the gene. We are now testing the possibility that they use a mixture of features to direct recombination because of changes in interacting genes that recruit the recombination machinery to sites of PRDM9 binding.