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Title: A whole-genome assembly of the domestic cow, Bos taurus

Author
item ZIMIN, ALEKSEY - University Of Maryland
item DELCHER, ARTHUR - University Of Maryland
item FLOREA, LILIANA - University Of Maryland
item KELLEY, DAVID - University Of Maryland
item SCHATZ, MICHAEL - University Of Maryland
item PUIU, DANIELA - University Of Maryland
item HANRAHAN, FINNIAN - University Of Maryland
item PERTEA, GEO - University Of Maryland
item Van Tassell, Curtis - Curt
item Sonstegard, Tad
item MARCAIS, GUILLAUME - University Of Maryland
item ROBERTS, MICHAEL - University Of Maryland
item SUBRAMANIAN, POORANI - University Of Maryland
item YORKE, JAMES - University Of Maryland
item SALZBERG, STEVEN - University Of Maryland

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2009
Publication Date: 4/24/2009
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.