About the Project
The genome of the Brown Norway rat (Rattus norvegicus) was sequenced by the Rat Genome Sequencing Consortium (RGSC), led by the HGSC. The RGSC was a collaboration with Celera Genomics, Genome Therapeutics (now Oscient Pharmaceuticals), The Institute for Genome Research (now J. Craig Venter Institute), The University of Utah, Children's Hospital Oakland Research Institute, Medical College of Wisconsin, and BC Genome Sciences Center. This rat is important as a model organism for cardiovascular and psychological research, and has a legacy of decades of study of its physiology in academia and industry.
The Brown Norway rat genome was analyzed and published in 2004 [PubMed]. A series of assemblies were produced:
| Assembly | Description |
|---|---|
| Rnor2.0 | first public release of Atlas rat assembly (11/02) |
| Rnor2.1 | update fixing duplication artifact, improvement to ultrabactig builds |
| Rnor3.0 | new assembly with new FPC map, more markers, 1100 additional BACs |
| Rnor3.1 | minor update (6/03) |
| Rnor3.2 | added 54 Mb finished sequence (10/04) |
| Rnor3.3 | minor update |
| Rnor3.4 | minor update (11/04) |
Rnor3.4 covers more than 90% of the estimated 2.8 Gb genome and is available for download using the FTP Data link in the sidebar on the right. This version incorporates 54.6 Mb of finished sequence into the draft genome assembly. Genome browsers for this data are listed in the resource section below. A brief description of the assembly is available.
The HGSC is currently upgrading the rat genome sequence through various activities. These include a new assembly that incorporates sequence from about 1,000 finished BAC clones, selected finishing of other regions of the genome, and sequencing of the Y chromosome. The HGSC is also sequencing eight other rat strains to low coverage for SNP discovery. In addition, ~1.5X coverage of rat reads were released by Celera Genomics and these are being used for SNP discovery.
Funding for the RGSC came from the National Heart, Lung, and Blood Institute (NHLBI) and the National Human Genome Research Institute (NHGRI) and subsequent activities are supported by the NHGRI.
Access to the Data
A graphical view of the rat genome coverage in BACs available here.
The BLAST link is located in the sidebar.
Individual matched sequences and the formatted BLAST database can be retrieved from the BCM FTP site at the link in the sidebar.
Overlapping BAC clones are arranged in Bactigs.
Information on a set of projects associated with a particular set of Quantitative Trait Loci (QTL) can be viewed by selecting the location of that marker (RAT-SA) from the QTL Browser.
A three-way comparison of human and mouse to rat chromosomes found using Pash is available for browsing.
International Genome Consortium Database
Resources
Upgrading the Rat Genome White Paper
Proposal for Discovering SNPs from Eight Commonly Used Inbred Rat Strains
Rat Genome Database - Medical College of Wisconsin
BAC Resources - Children's Hospital Oakland Research Institute
Genome Browsers - NCBI, UCSC, Ensembl, LBL
Selected PubMed Citations
Twigger, SN, Pruitt, KD, Fernandez-Suarez, XM, Karolchik, D, Worley, KC, Maglott, DR, Brown, G, Weinstock, G, Gibbs, RA et al. What everybody should know about the rat genome and its online resources. Nat. Genet. 2008 May; 40(5):523-7. [PubMed]
Worley, KC, Weinstock, GM, Gibbs, RA. Rats in the genomic era. Physiol. Genomics 2008 Feb 19; 32(3):273-82. [PubMed]
Gibbs, RA, Weinstock, GM, Metzker, ML, Muzny, DM, Sodergren, EJ, Scherer, S, Scott, G, Steffen, D, Worley, KC et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004 Apr 1; 428(6982):493-521. [PubMed]
