Deep WGS sequencing of hybrid B6CASTF1-PRDM9 Humanized/CAST mice

To examine mammalian non-crossover meiotic recombination with unprecedented resolution genome-wide, we intercrossed two highly diverged inbred mouse strains, C57BL/6J (B6) and CAST/Eij (CAST), for 5 generations and deeply sequenced the genomes of their recombinant offspring. We also controlled the PRDM9 alleles in these mice, selecting for a humanized PRDM9 allele engineered in the B6 parents, in order to study the effects of genetic diversity on recombination outcomes, independent of prior evolutionary effects due to hotspot erosion. In total, we sequenced 121 mice: one B6-PRDM9_Hum/Hum F0 mouse, one CAST-PRDM9_Cast/Cast F0 mouse, 11 F2 mice, and 18 F4/F5 families (36 F4 parents and 72 F5 offspring, all homozygous for PRDM9_Hum). We obtained coverage of ~10x for the F0/F4 mice, and ~20x for the F2 and F5 mice via the Illumina Hiseq2500 (F0 and 4 F2 mice) or Hiseq4000 platforms (remaining mice).