Whole-genome sequencing

New whole-genome sequence data were generated for 87 N2 progeny of the WSB/EiJ × PWK/PhJ cross at the University of North Carolina High-Throughput Sequencing Facility. Genomic DNA was fragmented by ultrasonication on a Covaris instrument (Covaris, Woburn, MA) and enriched for fragments ∼300 bp in size on a PippinPrep system (Sage Science, Beverly, MA). Paired-end libraries were prepared using the Illumina TruSeq PE v1 chemistry. Samples were multiplexed in two pools (with 45 and 42 samples, respectively) and sequenced 2 × 100 bp on an Illumina HiSeq 2500 instrument to a depth of ∼5×. Demultiplexing and postprocessing were performed with Illumina CASAVA v1.8.2. Data has been submitted to the European Nucleotide Archive (accession PRJEB32247).

Reads for inbred strains PWK/PhJ, FVB/NJ, and WSB/EiJ were obtained from the public FTP site of the Sanger Mouse Genomes Project, February 2015 release (ftp://ftp-mouse.sanger.ac.uk/REL-1502-BAM) (Keane et al. 2011). Reads for CC strains CC001/Unc, CC022/GeniUnc, CC032/GeniUnc, CC044/GeniUNC, and CC045/GeniUnc were generated by our research group and have been previously published (European Nucleotide Archive accession PRJEB14673) (Srivastava et al. 2017). Reads for wild M. musculus and M. spretus have been previously published (Harr et al. 2016), and were obtained from the European Nucleotide Archive (accessions PRJEB9450, PRJEB11742, PRJEB14167, and PRJEB2176). Reads for M. spicilegus have been previously published (Neme and Tautz 2016) and were obtained from the European Nucleotide Archive (accession PRJEB11513). Reads for M. caroli have been previously published (Thybert et al. 2018) and were obtained from the European Nucleotide Archive (accession PRJEB14895). A complete list of samples used in whole-genome sequencing analysis is provided in File S4.

The standard mouse reference assembly is a haploid representation of the genome, except in the PAR, whose sequence appears on both sex chromosomes. This induces ambiguous sequence alignments and effectively halves the observed read depth over each copy of the PAR. To avoid these artifacts, we masked the sequence of the Y PAR (chromosome Y:90745845–91644698) in the mm10/GRCm38 assembly with Ns. Reads were aligned to this masked reference with bwa mem 0.7.15-r1140 (Li 2013) with flags -t 16 -YK100000000 and default settings otherwise. Optical duplicates were marked with samblaster v0.1.24 (Faust and Hall 2014).