ArticleCell genomics2024
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.
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Article in Cell genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29citing papers in PubMed
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Who cites it
29 citing papers in PubMed.
- Transcriptomic Features of Thyroid Signaling Disorders in Experimental Pulmonary Arterial Hypertension.Bulletin of experimental biology and medicine · 2026Article
- Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats.bioRxiv : the preprint server for biology · 2026Article
- Rodent Models of Alzheimer's Disease: Bridging the Translational Gap Through Systems-Level Integration.Biomedicines · 2026Review
- Genetic Architecture of Addiction-Relevant Behaviors in Outbred Sprague-Dawley Rats Reveals Loci for Anxiety-Like and Nociceptive Traits.Genes, brain, and behavior · 2026Article
- Genome-Wide Annotation of Promoter-Enhancer Interactions via Chromatin Loops in the Hybrid Rat Diversity Panel.bioRxiv : the preprint server for biology · 2026Article
- BAT: an integrated pipeline for gene tree construction, annotation, and functional inference.bioRxiv : the preprint server for biology · 2026Article
- Oxycodone self-administration and genetic background exert community-specific effects in the gut microbiome.Scientific reports · 2026Article
- Article
- Genetic Architecture of Addiction-Relevant Behaviors in Outbred Sprague-Dawley Rats Reveals Loci for Anxiety-Like and Nociceptive Traits.bioRxiv : the preprint server for biology · 2026Article
- Long-read whole-genome sequencing of SHR rat substrains with distinct substance use phenotypes.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Hi-C sequencing data from frontal cortex of laboratory rats.Scientific data · 2025Article
- Unique Transcriptomic Cell Types of the Granular Retrosplenial Cortex Are Preserved across Mice and Rats despite Dramatic Changes in Key Marker Genes.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Perinatal fentanyl exposure drives enduring addiction risk and central amygdala gene dysregulation.Neuropharmacology · 2025Article
- Integrative multi-omics uncovers skeletal muscle enhancer programming of cardiorespiratory fitness.bioRxiv : the preprint server for biology · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Advanced Multiscale Attention Network for Estrous Cycle Stage Identification from Rat Vaginal Cytology.Biology · 2025Article
- Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation.Genome research · 2025Review
- Genetic modulation of protein expression in rat brain.iScience · 2025Article
- Establishing the hybrid rat diversity program: a resource for dissecting complex traits.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Pangenome reconstruction in rats enhances genotype-phenotype mapping and variant discovery.iScience · 2025Article
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Authors and funding
51 authors.
Tristan V de JongDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Yanchao PanDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
Pasi RastasInstitute of Biotechnology, University of Helsinki, Helsinki, Finland.
Daniel MunroDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA.
Monika TutajDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
Huda AkilMichigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
Chris BennerDepartment of Medicine, University of California San Diego, San Diego, CA, USA.
Denghui ChenDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Apurva S ChitreDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
William ChowTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Vincenza ColonnaInstitute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Clifton L DalgardDepartment of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
Wendy M DemosDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
Peter A DorisThe Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA.
Erik GarrisonDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Aron M GeurtsDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
Hakan M GunturkunDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Victor GuryevGenome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands.
Thibaut HourlierEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK.
Kerstin HoweTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Jun HuangDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Ted KalbfleischGluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA.
Panjun KimDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Ling LiDepartment 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.
Spencer MahaffeyDepartment of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Fergal J MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK.
Pejman MohammadiCenter for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.
Ayse Bilge OzelDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
Oksana PolesskayaDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Michal PravenecInstitute of Physiology, Czech Academy of Sciences, Prague, Czechia.
Pjotr PrinsDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Jonathan SebatDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Jennifer R SmithDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
Leah C Solberg WoodsDepartment of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
Boris TabakoffDepartment of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Alan TraceyTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Marcela Uliano-SilvaTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Flavia VillaniDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Hongyang WangDepartment of Animal Sciences, Washington State University, Pullman, WA, USA.
Burt M SharpDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Francesca TeleseDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Zhihua JiangDepartment of Animal Sciences, Washington State University, Pullman, WA, USA.
Laura SabaDepartment of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Xusheng WangDepartment 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.
Terence D MurphyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Abraham A PalmerDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
Anne E KwitekDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
Melinda R DwinellDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
Robert W WilliamsDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Jun Z LiDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, USA. Electronic address: junzli@med.umich.edu.
Hao ChenDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA. Electronic address: hchen@uthsc.edu.
Funding
National Biomedical Information ServicesZIHLM200888 · NLM · NATIONAL LIBRARY OF MEDICINE · PI PALTOO, DINA · 2009 to 2025
$5200.7MRAT GENOME DATABASER01HL064541 · NHLBI · MEDICAL COLLEGE OF WISCONSIN · PI ANNE E. KWITEK · 1999 to 2026
$50.0MText mining in the CloudU24HG010859 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAROL J BULT, PAUL Warren STERNBERG · 2019 to 2026
$42.0MSequencing CoreP50DA037844 · NIDA · UNIVERSITY OF CHICAGO · PI PALMER, ABRAHAM A · 2014 to 2023
$27.4MThe Heritable Transcriptome and AlcoholismR24AA013162 · NIAAA · UNIVERSITY OF COLORADO DENVER · PI HOFFMAN, PAULA, SABA, LAURA MAREN · 2001 to 2021
$14.2MSequencing Coordination and Data Analysis CoreP01HL149620 · NHLBI · UNIVERSITY OF ARIZONA · PI LIANG, MINGYU · 2020 to 2024
$11.8MInvestigating the role of Bmp4 in glial subtype specification and temperamentU01DA043098 · NIDA · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI HUDA AKIL, Jun Li · 2017 to 2026
$6.9MHybrid Rat Diversity Program - Import of HXB/BXH panelR24OD024617 · OD · MEDICAL COLLEGE OF WISCONSIN · PI DWINELL, MELINDA R · 2018 to 2025
$6.8MSingle-cell resolution analysis of chromatin accessibility and gene expression changes in a model of drug addictionU01DA050239 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GRAHAM MCVICKER, Abraham A Palmer · 2020 to 2026
$4.4MTIM Project NIDA P30 CenterP30DA044223 · NIDA · UNIVERSITY OF TENNESSEE HEALTH SCI CTR · PI SEN, SAUNAK · 2017 to 2021
$3.9MThe role of structural variants and tandem repeats in substance abuse-related behavioral traitsU01DA051234 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GYMREK, MELISSA, PALMER, ABRAHAM A · 2021 to 2025
$3.5MDecoding the grammar of transcriptional enhancers regulating different stages of opioid use disorderU01DA051972 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BENNER, CHRISTOPHER W, TELESE, FRANCESCA · 2020 to 2024
$3.4MNHGRI NIH HHS R01 HG011252NHGRI NIH HHS U24 HG010859NHLBI NIH HHS P01 HL149620NHLBI NIH HHS R01 HL064541NIAAA NIH HHS R24 AA013162NIDA NIH HHS P30 DA044223NIDA NIH HHS P50 DA037844NIDA NIH HHS R01 DA048017NIDA NIH HHS U01 DA043098NIDA NIH HHS U01 DA047638NIDA NIH HHS U01 DA050239NIDA NIH HHS U01 DA051234NIDA NIH HHS U01 DA051972NIGMS NIH HHS R01 GM134366NIGMS NIH HHS R01 GM140287NIH HHS R24 OD024617Wellcome Trust
Abstract
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.
Indexed as
GenomeGenomicsAnimalsGenetic VariationMolecular Sequence AnnotationRatsWhole Genome Sequencinggenetic mapheterogeneous stockhybrid rat diversity panelinbred strainsmRatBN7.2phylogenetic treeratrecombinant inbredreference genomeRnor_6.0
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