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

Autor:	de Jong TV; Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA., Pan Y; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA., Rastas P; Institute of Biotechnology, University of Helsinki, Helsinki, Finland., 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., Tutaj M; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA., Akil H; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA., Benner C; Department of Medicine, University of California San Diego, San Diego, CA, USA., Chen D; Department of Psychiatry, University of California San Diego, San Diego, CA, USA., Chitre AS; Department of Psychiatry, University of California San Diego, San Diego, CA, USA., Chow W; Tree of Life, Wellcome Sanger Institute, Cambridge, UK., 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., Dalgard CL; Department of Anatomy, Physiology & Genetics; The American Genome Center, Uniformed Services University of the Health Sciences, Washington DC, USA., Demos WM; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA., Doris PA; The Brown Foundation Institute of Molecular Medicine, Center For Human Genetics, University of Texas Health Science Center, Houston, TX, USA., Garrison E; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA., Geurts AM; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA., Gunturkun HM; Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA., Guryev V; Genome Structure and Ageing, University of Groningen, UMC Groningen, The Netherlands., Hourlier T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK., Howe K; Tree of Life, Wellcome Sanger Institute, Cambridge, UK., Huang J; Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA., Kalbfleisch T; Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA., Kim P; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA., 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., Mahaffey S; Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Martin FJ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK., 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., Ozel AB; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA., Polesskaya O; Department of Psychiatry, University of California San Diego, San Diego, CA, USA., Pravenec M; Institute of Physiology, Czech Academy of Sciences, Prague, Czechia., Prins P; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA., Sebat J; Department of Psychiatry, University of California San Diego, San Diego, CA, USA., Smith JR; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA., Solberg Woods LC; Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA., Tabakoff B; Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Tracey A; Tree of Life, Wellcome Sanger Institute, Cambridge, UK., Uliano-Silva M; Tree of Life, Wellcome Sanger Institute, Cambridge, UK., Villani F; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA., Wang H; Department of Animal Sciences, Washington State University, Pullman, WA, USA., Sharp BM; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA., Telese F; Department of Psychiatry, University of California San Diego, San Diego, CA, USA., Jiang Z; Department of Animal Sciences, Washington State University, Pullman, WA, USA., Saba L; Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., 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., Murphy TD; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA., 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., Kwitek AE; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA., Dwinell MR; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA., Williams RW; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA., Li JZ; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA., Chen H; Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2023 Sep 28. Date of Electronic Publication: 2023 Sep 28.
DOI:	10.1101/2023.04.13.536694
Abstrakt:	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 to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. 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 18.7 thousand 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. Competing Interests: Declaration of interests The authors declare no competing interests.
Databáze:	MEDLINE
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