Comparative Genomics in Rodents: Insights into Reproductive Isolation Genes

Comparative genomics is an useful tool for identifying genes involved in reproductive isolation and in determining in which degree chromosomal rearrangements act as an impermeable barrier to gene flow, facilitating the accumulation of genetic incompatibilities that will, in the long term, contributing to speciation. In this work, we established whole-genome comparisons of eleven mammalian species, including five rodent species, to define the evolutionary genomic landscape in the mouse genome.  We detected regions of conserved synteny (HSBs) and novel lineage and clade-specific evolutionary breakpoint regions (EBRs) within Rodentia. We observed an accumulation of protein-coding genes in EBRs; especially genes implicated in reproduction isolation, such as Krueppel genes, a group of transcription factors with zinc finger (ZnF) domains, among which the Prdm9 gene is the most representative. Moreover, and given the role of this gene in hybrid sterility, we study the evolutionary constrains that may affect the Prdm9 gene across a natural population of house mice with chromosomal fusions in polymorphic state. Our results reveal an extreme allelic diversity in both ZnF copy number and sequence with the characterization of 12 different alleles in a population of 172 mice. The analysis of meiotic recombination in a subset of these mice reveals that mean recombination rates were positively correlated with a decrease in the number of ZnF domains. Overall, the presence of genes related to species-specific phenotypes (such as reproductive isolation) and low recombination rates in EBRs reinforces the adaptive value of genome reshuffling.