Journal
BMC GENOMICS
Volume 10, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1471-2164-10-180
Keywords
-
Funding
- National Institutes of Health (NIH), U.S. Department of Health and Human Services [U54 HG003273]
- U.S. Department of Agriculture's Agricultural Research Service (USDA ARS) [59-0790-3-196]
- Cooperative State Research, Education, and Extension Service National Research Initiative [2004-35216-14163]
- state of Texas
- The Research Council of Norway
- Genome Canada through Genome British Columbia
- The Alberta Science and Research Authority
- The Commonwealth Scientific and Industrial Research Organization of Australia (CSIRO)
- Agritech Investments Ltd.
- Dairy Insight, Inc.
- AgResearch Ltd.
- Research Council of Norway
- Robert J. Klebert, Jr. and Helen C. Kleberg Foundation
- National, Texas and South Dakota Beef Checkoff Funds
Ask authors/readers for more resources
Background: We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. Results: The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. Conclusion: The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available