About the Project
The Human Genome Sequencing Center is working to sequence and annotate the bovine genome, Bos taurus. The bovine genome assembly and analysis and the study of cattle genetic history were published in April 24, 2009 issue of Science.
Sequencing of the bovine (Hereford) genome consumed a large part of 2004-06 HGSC resources. The project was staged to produce an initial 3x WGS assembly followed by a second 6x WGS assembly to allow gene predictions for preliminary annotation, and a final assembly including BAC sequences for improved local assembly refinement. The 3x assembly was used by Ensembl to test their pipeline on low coverage genome assemblies. The 6x WGS assembly was released and gene predictions from Ensembl and NCBI have been made public. The final assembly has been completed using the Atlas assembler and BAC data from equal numbers of BACs sequenced individually or by the CAPSS clone pooling strategy.
WGS samples from six other breeds were sequenced to identify SNPs for genetic studies. A panel of 10,000 SNPs were mined at the HGSC from this interbreed dataset and genotyping reagents were developed. 227 animals representing 9 breeds were genotyped and analyzed. An expanded set of markers (32,000) was applied to a more extensive group of animals (449). The results form the basis of a Bovine HapMap Project. Affymetrix now markets a bovine genotyping chip based on this work, allowing broader translation of the genome project into applications.
A meeting of sixty bovine researchers in Houston in March 2005 began coordination for overall genome analysis and the future of bovine research. A working group for annotation selected themes for analysis (Global analyses; Muscle, Immune function; Lactation; Energy partitioning, Metabolism, Rumen function; Reproduction, Endocrinology, Sex determination, Development; Imprinted genes, HDACs, Methyl transferases; Bovine models of human diseases; Non-coding RNA; Genetics/Genotyping; Behavior, Maternal nurturing; Prion protein). The Bovine Genome Project leveraged NHGRI funds with funds from other sources. This allowed the utility of the sequence to be enhanced by genetic analysis, outside the scope of the standard basic genome project deliverables.
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 |
|---|---|---|---|
| 2009 April 15 | Btau_4.2 | 7.1x | Draft assembly replaced with high quality finished sequence where available. |
| 2007 Oct 01 | Btau_4.0 | 7.1x | Draft assembly, using Whole Genome Shotgun (WGS) reads from small insert clones and BAC sequences from BACs sequenced individually or by the CAPSS clone pooling strategy. Mapped to chromosomes using refined mapping information. |
| 2006 Aug 15 | Btau_3.1 | 7.1x | Draft assembly, using Whole Genome Shotgun (WGS) reads from small insert clones and BAC sequences from BACs sequenced individually or by the CAPSS clone pooling strategy. |
| 2005 Mar 10 | Btau_2.0 | 6.2x | Preliminary assembly, using WGS reads from small insert clones and BAC end sequences. |
| 2004 Sep 27 | Btau_1.0 | 3x | Preliminary assembly, using WGS reads from small insert clones |
Access to the Data
The final draft assembly (7.1 coverage) and the two previous assemblies are available for download as contigs or linearized scaffolds by using the FTP Data link in the sidebar. The assemblies are described in more detail in the README files.
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
Photo by Michael MacNeil, USDA
| 2009 Apr 24 |
| Bovine genome publication |
| by Bovine Genome Sequencing and Analysis Consortium |
| 2009 Apr 15 |
| Bovine genome assembly |
| v.4.2 |
| 2007 Oct 01 |
| Bovine genome assembly |
| v.4.0 |
| 2006 Aug 15 |
| Bovine genome assembly |
| v.3.1 |