Browsing by Author "Florea, Liliana"

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    A whole-genome assembly of the domestic cow, Bos taurus
    (2009-04-29) 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; Marcais, 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.