Open Access Highly Accessed Research

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

Aleksey V Zimin1, Arthur L Delcher2, Liliana Florea2, David R Kelley2, Michael C Schatz2, Daniela Puiu2, Finnian Hanrahan2, Geo Pertea2, Curtis P Van Tassell3, Tad S Sonstegard3, Guillaume Marçais1, Michael Roberts1, Poorani Subramanian1, James A Yorke1 and Steven L Salzberg2*

Author Affiliations

1 Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA

2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA

3 Agricultural Research Service, U.S. Department of Agriculture, 10300 Baltimore Ave., Beltsville, Maryland 20705, USA

For all author emails, please log on.

Genome Biology 2009, 10:R42  doi:10.1186/gb-2009-10-4-r42

Published: 24 April 2009

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.