A whole-genome assembly of the domestic cow, Bos taurus
2009
Zimin, Aleksey V | Delcher, Arthur L. | Florea, Liliana | Kelley, David R | Schatz, Michael C | Puiu, Daniela | Hanrahan, Finnian | Pertea, Geo | Van Tassell, Curtis P | Sonstegard, Tad S | Marçais, Guillaume | Roberts, Michael | Subramanian, Poorani | Yorke, James A. | Salzberg, Steven L
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.
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