Population and subspecies diversity at mouse centromere satellites

Abstract Background Mammalian centromeres are satellite-rich chromatin domains that execute conserved roles in kinetochore assembly and chromosome segregation. Centromere satellites evolve rapidly between species, but little is known about population-level diversity across these loci. Results We developed a k -mer based method to quantify centromere copy number sequence variation from whole genome sequencing data. applied this diverse inbred wild house mouse ( Mus musculus ) genomes profile the core (minor) satellite pericentromeric (major) repeat. show minor varies more than 10-fold among strains, whereas major numbers span 3-fold range. In contrast widely held assumptions homogeneity of repeats, we uncover marked heterogeneity within single genomes, with levels exceeding those at satellite. Analyses wild-caught mice implicate subspecies population origin as significant determinants heterogeneity. Intriguingly, also find harbor dramatically reduced elevated compared suggesting inbreeding may reshape architecture pronounced ways. Conclusion Taken together, our results highlight power approaches for probing repetitive regions, provide an initial portrait musculus, lay groundwork future functional studies on consequences natural genetic essential domains.