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Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Gibbs, Richard A. and Pachter, Lior (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428 (6982). pp. 493-521. ISSN 0028-0836. doi:10.1038/nature02426. https://resolver.caltech.edu/CaltechAUTHORS:20170308-145138306

[img] MS Word (Supplementary Information. Additional history of the rat, rat genetics, and the rat genome sequencing project) - Supplemental Material
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[img] PDF (Supplementary Figure 1. BAC clone selection process) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 2. Coverage of finished BACs based on depth of BAC bait coverage) - Supplemental Material
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[img] PDF (Supplementary Figure 3. Partitioning of the Fingerprint and YAC map contigs against the rat sequence assembly) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 4. Coverage of BAC clones selected for sequencing from the fingerprint map) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 5. Correlation of SINE locations in rat and mouse) - Supplemental Material
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[img] PDF (Supplementary Figure 6. Dot-plots showing positions of aligning segments in rat-rat, rat-mouse, and rat-human comparisons, for a 10 Mb region of rat Chromosome 10 and the orthologous regions in mouse and human) - Supplemental Material
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[img] PDF (Supplementary Figure 7. Sequence conservation at AG acceptor splice sites in aligned introns) - Supplemental Material
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[img] PDF (Supplementary Figure 8. Sequence conservation at GT donor splice sites in aligned introns) - Supplemental Material
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Abstract

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/nature02426DOIArticle
http://www.nature.com/nature/journal/v428/n6982/full/nature02426.htmlPublisherArticle
http://rdcu.be/pU15PublisherFree ReadCube access
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2004 Macmillan Publishers Limited. Received 31 December 2003; Accepted 20 February 2004. Work at Baylor College of Medicine was supported by a grant from the NHGRI and NHLBI to R.A.G. Work at Genome Therapeutics was supported by grants from the NHGRI to D.S. A.S. acknowledges support from the NIGMS. M.B. acknowledges support from the NIH. N.H. was supported by the NGFN/BMBF (German Ministry for Research and Education). B.J.T. and J.M.Y. are supported by an NIH grant from the NIDCD. K.M.R. and G.M.C. are Howard Hughes Medical Institute Predoctoral Fellows. L.M.D'S., K.M. and K.J.K. are supported by training fellowships from the W. M. Keck Foundation to the Gulf Coast Consortia through the Keck Center for Computational and Structural Biology. Work at Case Western Reserve was supported in part by NIH grants to E.E.E. Work at IMIM was supported by a grant from Plan Nacional de I + D (Spain). M.M.A. acknowledges support from programme Ramón y Cajal and a grant from the Spanish Ministry of Science and Technology. Work at Universidad de Oviedo was supported by grants from the European Union, Obra Social Cajastur and Gobierno del Principado de Asturias. Work at Penn State University was supported by NHGRI grants. Work at the University of California Berkeley was supported by a grant from the NIH. Work at the Washington University School of Medicine Genome Sequencing Center and the British Columbia Cancer Agency Genome Sciences Centre was supported by an NIH grant. Work at UCSC and CHORI was supported by the NHGRI. The author declares no competing financial interests.
Funders:
Funding AgencyGrant Number
National Human Genome Research InstituteUNSPECIFIED
National Heart, Lung, and Blood InstituteUNSPECIFIED
National Institute of General Medical SciencesUNSPECIFIED
Bundesministerium für Bildung und Forschung (BMBF)UNSPECIFIED
NIHUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
W. M. Keck FoundationUNSPECIFIED
Plan Nacional de I + D (Spain)UNSPECIFIED
Ramón y Cajal ProgrammeUNSPECIFIED
Ministerio de Ciencia y Tecnología (MYCT)UNSPECIFIED
European UnionUNSPECIFIED
Obra Social CajasturUNSPECIFIED
Gobierno del Principado de AsturiasUNSPECIFIED
Issue or Number:6982
DOI:10.1038/nature02426
Record Number:CaltechAUTHORS:20170308-145138306
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170308-145138306
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74926
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:09 Mar 2017 15:32
Last Modified:15 Nov 2021 16:29

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