A Whole-Genome Assembly of the Domestic Cow, Bos taurus

Authors

• Aleksey V. Zimin, University of Maryland, College Park
• Arthur L. Delcher, University of Maryland, College Park
• Liliana Florea, University of Maryland, College Park
• David R. Kelley, University of Maryland, College Park
• Michael C. Schatz, University of Maryland, College Park
• Daniela Puiu, University of Maryland, College Park
• Finnian Hanrahan, University of Maryland, College Park
• Geo Pertea, University of Maryland, College Park
• Curtis P. Van Tassell, USDA-ARSFollow
• Tad S. Sonstegard, USDA-ARS
• Guillaume Marçais, University of Maryland, College Park
• Michael Roberts, University of Maryland, College Park
• Poorani Subramanian, University of Maryland, College Park
• James A. Yorke, University of Maryland, College Park
• Steven. L Salzberg, University of Maryland, College Park

Document Type

Article

Date of this Version

2009

Comments

Published in Genome Biology 2009, 10:R42 (doi:10.1186/gb-2009-10-4-r42).

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.