The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

Center for Immunity and Immunotherapies Seattle Children's Research Institute Seattle WA USA; Department of Pediatrics University of Washington School of Medicine Seattle WA USA

Department of Anatomy Physiology and Genetics The American Genome Center Uniformed Services University of the Health Sciences Bethesda MD USA

Department of Animal Sciences Washington State University Pullman WA USA

Department of Genetics Genomics and Informatics University of Tennessee Health Science Center Memphis TN USA

Department of Genetics Genomics and Informatics University of Tennessee Health Science Center Memphis TN USA; Center for Proteomics and Metabolomics St Jude Children's Research Hospital Memphis TN USA

Department of Human Genetics University of Michigan Ann Arbor MI USA

Department of Internal Medicine Section on Molecular Medicine Wake Forest University School of Medicine Winston Salem NC USA

Department of Medicine University of California San Diego San Diego CA USA

Department of Pharmaceutical Sciences Skaggs School of Pharmacy and Pharmaceutical Sciences University of Colorado Anschutz Medical Campus Aurora CO USA

Department of Pharmacology Addiction Science and Toxicology University of Tennessee Health Science Center Memphis TN USA

Department of Physiology Medical College of Wisconsin Milwaukee WI USA

Department of Physiology Medical College of Wisconsin Milwaukee WI USA; Rat Genome Database Medical College of Wisconsin Milwaukee WI USA

Department of Psychiatry University of California San Diego San Diego CA USA

Department of Psychiatry University of California San Diego San Diego CA USA; Department of Integrative Structural and Computational Biology Scripps Research San Diego CA USA

Department of Psychiatry University of California San Diego San Diego CA USA; Institute for Genomic Medicine University of California San Diego La Jolla CA USA

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus in Hinxton Cambridgeshire UK

Genome Structure and Ageing University of Groningen UMC Groningen the Netherlands

Gluck Equine Research Center Department of Veterinary Science University of Kentucky Louisville KY USA

Institute of Biotechnology University of Helsinki Helsinki Finland

Institute of Genetics and Biophysics National Research Council Naples Italy; Department of Genetics Genomics and Informatics University of Tennessee Health Science Center Memphis TN USA

Institute of Physiology Czech Academy of Sciences Prague Czechia

Michigan Neuroscience Institute University of Michigan Ann Arbor MI USA

National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda MD USA

The Brown Foundation Institute of Molecular Medicine Center for Human Genetics University of Texas Health Science Center Houston TX USA

Tree of Life Wellcome Sanger Institute Cambridge UK

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bioRxiv. 2023 Sep 28:2023.04.13.536694. doi: 10.1101/2023.04.13.536694. PubMed

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Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery