Bovine Genome Project
Bovine Genome Project
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Milestones and BCM-HGSC data July 2012—Btau 4.6.1 October 2009—Btau 4.5 April 2009—Btau 4.2 October 2007—Btau 4.0 August 2006—Btau 3.1 March 2005—Btau 2.0 September 2004—Btau 1.0 Links |
About the Project
The BCM-HGSC sequenced and analyzed the bovine genome (Bos taurus). The initial bovine genome assembly and analysis and the study of cattle genetic history were published April 24, 2009. Ongoing efforts to improve the genome are centered around finishing the Y chromosome.
The source of the BAC library DNA was Hereford bull L1 Domino 99375, registration number 41170496. Dr. Michael MacNeil's laboratory, USDA-ARS, Miles City, MT, provided the blood. The DNA for the whole genome shotgun sequences was provided by Dr. Timothy Smith's laboratory, U.S. Meat Animal Research Center, Clay Center, NE, from white blood cells from L1 Dominette 01449, American Hereford Association registration number 42190680 (a daughter of L1 Domino 99375). A skin cell fibroblast cell line from the same animal is available from Dr. Carol Chitko-McKown's laboratory, although there is no sequence from that cell line.
Funding for this project has been provided by: the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH); the U.S. Department of Agriculture's Agricultural Research Service and Cooperative State Research, Education, and Extension Service (USDA ARS Agreement No. 5 9-0790-3-196 and CSREES Agreement No. 2004-35216-14163); the state of Texas; Genome Canada through Genome British Columbia, The Commonwealth Scientific and Industrial Research Organization of Australia (CSIRO); Agritech Investments Ltd., Dairy Insight, Inc. and AgResearch Ltd., all of New Zealand; the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation; and the National, Texas and South Dakota Beef Check-off Funds.
Genome Assemblies
| Date Released | Release Name | Coverage | Comments |
|---|---|---|---|
| July 2012 | Btau_4.6.1 | Draft assembly replaced data in Btau_4.5 with high quality finished data where available. | |
| October 2009 | Btau_4.5 | Draft assembly incorporating additional Whole Genome Shotgun (WGS) contigs from Btau_2.0 into Btau_4.0 | |
| April 2009 | Btau_4.2 | 7.1x | Draft assembly Btau_4.0 data replaced with high quality finished sequence where available. |
| October 2007 | Btau_4.0 | 7.1x | Draft assembly using (WGS) reads from small insert clones and BAC sequences. Mapped to chromosomes using refined mapping information. |
| August 2006 | Btau_3.1 | 7.1x | Draft assembly (WGS) reads from small insert clones and BAC sequences. |
| March 2005 | Btau_2.0 | 6.2x | Preliminary assembly using (WGS) reads from small insert clones and BAC end sequences. |
| September 2004 | Btau_1.0 | 3x | Preliminary assembly using (WGS) reads from small insert clones. |
Access to the Data
Genome Assembly
The final draft assembly (7.1 coverage) and the two previous assemblies are available for download as contigs or linearized scaffolds by using the BCM-HGSC data links in the sidebar. The assemblies are described in more detail in the README files.
BLAST Searches
HGSC provides BLAST searches of the genome assemblies, either as contigs or as linearized chromosome sequences. The WGS sequence enriched BAC assemblies and the unassembled reads (sequencing reads that did not end up in the genome assembly) can also be searched by BLAST. The BLAST link is located in the sidebar.
Traces are available from the NCBI Trace Archive by using the link in the sidebar or by using NCBI MegaBLAST with a same species or cross species query.
Resources
BAC Resources—Children's Hospital Oakland Research Institute
Bovine BAC fingerprint map at University of British Columbia
International Genome Consortium Database
Selected PubMed Citations
Liu, Y, Qin, X, Song, XZ, Jiang, H, Shen, Y, Durbin, KJ, Lien, S, Kent, MP, Sodeland, M et al. Bos taurus genome assembly. BMC Genomics 2009; 10():180. [PubMed]
Bovine HapMap Consortium, Gibbs, RA, Taylor, JF, Van Tassell, CP, Barendse, W, Eversole, KA, Gill, CA, Green, RD, Hamernik, DL et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 2009 Apr 24; 324(5926):528-32. [PubMed]
Bovine Genome Sequencing and Analysis Consortium, Elsik, CG, Tellam, RL, Worley, KC, Gibbs, RA, Muzny, DM, Weinstock, GM, Adelson, DL, Eichler, EE et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009 Apr 24; 324(5926):522-8. [PubMed]
Cai WW, Chen R, Gibbs RA, Bradley A., A clone-array pooled shotgun strategy for sequencing large genomes. Genome Res. 2001 Oct;11(10):1619-23. [PubMed]