A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

Rnor_6.0 genetic map heterogeneous stock hybrid rat diversity panel inbred strains mRatBN7.2 phylogenetic tree rat recombinant inbred reference genome

Journal

Cell genomics
ISSN: 2666-979X
Titre abrégé: Cell Genom
Pays: United States
ID NLM: 9918284260106676

Informations de publication

Date de publication:
22 Mar 2024
Historique:
received: 02 10 2023
revised: 26 12 2023
accepted: 29 02 2024
medline: 28 3 2024
pubmed: 28 3 2024
entrez: 27 3 2024
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1016/j.xgen.2024.100527 PMID: 38537634
pubmed: 38537634
pii: S2666-979X(24)00069-7
doi: 10.1016/j.xgen.2024.100527
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

100527

Informations de copyright

Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests The authors declare no competing interests.

Auteurs

Tristan V de Jong (TV)

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

Yanchao Pan (Y)

Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.

Pasi Rastas (P)

Institute of Biotechnology, University of Helsinki, Helsinki, Finland.

Daniel Munro (D)

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.

Monika Tutaj (M)

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

Huda Akil (H)

Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.

Chris Benner (C)

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

Denghui Chen (D)

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

Apurva S Chitre (AS)

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

William Chow (W)

Tree of Life, Wellcome Sanger Institute, Cambridge, UK.

Vincenza Colonna (V)

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.

Clifton L Dalgard (CL)

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

Wendy M Demos (WM)

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

Peter A Doris (PA)

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

Erik Garrison (E)

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

Aron M Geurts (AM)

Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.

Hakan M Gunturkun (HM)

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

Victor Guryev (V)

Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands.

Thibaut Hourlier (T)

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

Kerstin Howe (K)

Tree of Life, Wellcome Sanger Institute, Cambridge, UK.

Jun Huang (J)

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

Ted Kalbfleisch (T)

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

Panjun Kim (P)

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

Ling Li (L)

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.

Spencer Mahaffey (S)

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

Fergal J Martin (FJ)

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

Pejman Mohammadi (P)

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.

Ayse Bilge Ozel (AB)

Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.

Oksana Polesskaya (O)

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

Michal Pravenec (M)

Institute of Physiology, Czech Academy of Sciences, Prague, Czechia.

Pjotr Prins (P)

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

Jonathan Sebat (J)

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

Jennifer R Smith (JR)

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

Leah C Solberg Woods (LC)

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

Boris Tabakoff (B)

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

Alan Tracey (A)

Tree of Life, Wellcome Sanger Institute, Cambridge, UK.

Marcela Uliano-Silva (M)

Tree of Life, Wellcome Sanger Institute, Cambridge, UK.

Flavia Villani (F)

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

Hongyang Wang (H)

Department of Animal Sciences, Washington State University, Pullman, WA, USA.

Burt M Sharp (BM)

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

Francesca Telese (F)

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

Zhihua Jiang (Z)

Department of Animal Sciences, Washington State University, Pullman, WA, USA.

Laura Saba (L)

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

Xusheng Wang (X)

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.

Terence D Murphy (TD)

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

Abraham A Palmer (AA)

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.

Anne E Kwitek (AE)

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

Melinda R Dwinell (MR)

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

Robert W Williams (RW)

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

Jun Z Li (JZ)

Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA. Electronic address: junzli@med.umich.edu.

Hao Chen (H)

Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA. Electronic address: hchen@uthsc.edu.

Classifications MeSH