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

Area of Science:

• Genomics
• Comparative genomics
• Molecular biology

Background:

• High-quality reference genomes are crucial for accurate genetic analysis.
• Previous mouse genome assemblies (e.g., GRCm39) had incomplete or unresolved regions.
• Understanding genetic variation across diverse mouse strains is essential for research.

Purpose of the Study:

• To generate a comprehensive collection of 17 high-quality, long-read inbred mouse strain genomes with complete annotation.
• To resolve previously unannotated or incomplete genomic regions, including the MHC, defensin, T cell receptor, and Ly49 complexes.
• To identify and localize non-reference genes and characterize variable number tandem repeats (VNTRs) across mouse strains.

Main Methods:

• Generation of long-read sequencing data for 17 inbred mouse strains.
• De novo genome assembly and annotation, focusing on resolving complex genomic regions.
• Genome-wide scanning for variable number tandem repeats (VNTRs) within coding regions.
• Comparative analysis of new genome annotations against the GRCm39 reference.

Main Results:

• A collection of 17 high-quality mouse genomes with contig N50s ranging from 0.8-33.9 Mbp.
• Resolution of previously incomplete genomic regions, including the MHC, defensin cluster, T cell receptor, and Ly49 complexes.
• Localization of hundreds of non-reference genes and identification of over 400 genes with coding VNTR polymorphisms.
• Demonstrated improvement in RNA sequencing (RNA-seq) analysis, with a 5.1% increase in read mapping and identification of expression differences in 2.1% of coding genes for PWK/PhJ.

Conclusions:

• The presented high-quality mouse genomes provide a significantly improved reference for genetic and genomic studies.
• Enhanced annotation and resolution of complex regions facilitate the discovery and characterization of novel genes and genetic variations.
• These new reference genomes substantially improve RNA sequencing analyses, enabling more accurate detection of gene expression differences and genetic polymorphisms across mouse strains.