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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: A whole-genome assembly of the domestic cow, Bos taurus

Authors
item Zimin, Aleksey -
item Delcher, Arthur -
item Florea, Liliana -
item Kelley, David -
item Schatz, Michael -
item Puiu, Daniela -
item Hanrahan, Finnian -
item Pertea, Geo -
item Van Tassell, Curtis
item Sonstegard, Tad
item Marcais, Guillaume -
item Roberts, Michael -
item Subramanian, Poorani -
item Yorke, James -
item Salzberg, Steven -

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 24, 2009
Publication Date: April 24, 2009
Citation: Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S., Marcais, G., Roberts, M., Subramanian, P., Yorke, J.A., Salzberg, S.L. 2009. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10(4):R42.

Interpretive Summary: The genome of the domestic cow, Bos Taurus, was sequenced. The raw sequence data is available in pubic databases, and is available for analysis and assembly. In this study, we collected all the sequences produced from this project, and created an alternative genome assembly using a different assembly algorithm. The results of this alternative assembly allowed us to make multiple improvements over previous assemblies by closing gaps, and removing erroneous inversions, deletions, and translocations. Our evaluation using independent metrics demonstrates that the resulting assembly is substantially more accurate and complete than alternative versions. This research paves the way to maintain a well-curated and continually improving assembly of the bovine genome that will be sued for continued genetic and functional genomic studies of cattle.

Technical Abstract: Background: The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods. Results: We have assembled the 35 million sequence reads and applied a variety of assembly improvement techniques, creating an assembly of 2.86 billion base pairs that has multiple improvements over previous assemblies: it is more complete, covering more of the genome; thousands of gaps have been closed; many erroneous inversions, deletions, and translocations have been corrected; and thousands of single-nucleotide errors have been corrected. Our evaluation using independent metrics demonstrates that the resulting assembly is substantially more accurate and complete than alternative versions. Conclusions: By using independent mapping data and conserved synteny between the cow and human genomes, we were able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. Taurus chromosomes. We constructed a new cow-human synteny map that expands upon previous maps. We also identified for the first time a portion of the B. taurus Y chromosome.

Last Modified: 7/28/2014