High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape

We present a collection of 17 high-quality long-read inbred mouse strain genomes with complete annotation (contig N50s of 0.8-33.9 Mbp). This collection includes 12 widely used classical laboratory strains and 5 wild-derived strains. We have resolved previously incomplete genomic regions, including the major histocompatibility complex (MHC), defensin cluster, T cell receptor, and Ly49 complexes. Hundreds of non-reference genes from previous publications not found in GRCm39, such as Defa1, Raet1a, and Klra20 (Ly49T), were localized in the new reference genomes. We conducted a genome-wide scan of variable number tandem repeats (VNTRs) within the coding regions, identifying over 400 genes with VNTR polymorphisms with up to 600 repeat copies and repeat units reaching 990 nucleotides. Our strain-specific annotations enhance RNA sequencing (RNA-seq) analyses, as demonstrated in PWK/PhJ, where we observed a 5.1% improvement in read mapping and expression-level differences in 2.1% of coding genes compared to using GRCm39.