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Bovine Genome Project

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. Later efforts centered around finishing the Y chromosome. The most recent efforts to improve the genome are using Pacific Biosciences long-read data. We have produced 19-fold coverage of long read sequence data and combined these with the existing genome assembly using the PBJelly2 software. A de novo genome assembly using higher coverage PacBio data is planned in collaboration with Timothy Smith and Juan Medrano.

The source of the BABovineC 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 (for the Sanger data) and spleen (for the PacBio data) 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.

Current improvement efforts are funded by the United States Department of Agriculture National Institute of Food and Agriculture (2013-67015-21228) with support from the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH). Past funding for this project was also provided by: NHGRI U54 HG003273 as well as 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.

Genomic Resources

Genome Assemblies

Date Released Release Name Coverage Comments
soon Btau_5.1 25x Improved draft assembly combined 19x PacBio data with UMD 3.1 using PBJelly.
July 2012 Btau_4.6.1 7.1x Draft assembly replaced data in Btau_4.5 with high quality finished data where available.
October 2009 Btau_4.5 7.1x 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.

Additional Resources

Project History (next page)

Related Publications

Bos taurus genome assembly., Liu, Yue, Qin Xiang, Song Xing-Zhi Henry, Jiang Huaiyang, Shen Yufeng, Durbin James K., Lien Sigbjørn, Kent Matthew Peter, Sodeland Marte, Ren Yanru, et al. , BMC genomics, 2009, Volume 10, p.180, (2009) Abstract
Unlocking the bovine genome., Tellam, Ross L., Lemay Danielle G., Van Tassell Curtis P., Lewin Harris A., Worley Kim C., and Elsik Christine G. , BMC genomics, 2009, Volume 10, p.193, (2009) Abstract
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse., Durfee, Tim, Nelson Richard, Baldwin Schuyler, Plunkett Guy, Burland Valerie, Mau Bob, Petrosino Joseph F., Qin Xiang, Muzny Donna M., Ayele Mulu, et al. , Journal of bacteriology, 2008 Apr, Volume 190, Issue 7, p.2597-606, (2008) Abstract
Comparative analysis of the bovine MHC class IIb sequence identifies inversion breakpoints and three unexpected genes., Childers, C. P., Newkirk H. L., Honeycutt D. A., Ramlachan N., Muzney D. M., Sodergren E., Gibbs R. A., Weinstock G. M., Womack J. E., and Skow L. C. , Animal genetics, 2006 Apr, Volume 37, Issue 2, p.121-9, (2006) Abstract
The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny., Gioia, Jason, Qin Xiang, Jiang Huaiyang, Clinkenbeard Kenneth, Lo Reggie, Liu Yamei, Fox George E., Yerrapragada Shailaja, McLeod Michael P., McNeill Thomas Z., et al. , Journal of bacteriology, 2006 Oct, Volume 188, Issue 20, p.7257-66, (2006) Abstract
Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps., Fjell, Christopher D., Bosdet Ian, Schein Jacqueline E., Jones Steven J. M., and Marra Marco A. , Genome research, 2003 Jun, Volume 13, Issue 6A, p.1244-9, (2003) Abstract
Software for automated analysis of DNA fingerprinting gels., Fuhrmann, Daniel R., Krzywinski Martin I., Chiu Readman, Saeedi Parvaneh, Schein Jacqueline E., Bosdet Ian E., Chinwalla Asif, Hillier Ladeana W., Waterston Robert H., McPherson John D., et al. , Genome research, 2003 May, Volume 13, Issue 5, p.940-53, (2003) Abstract
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