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

Aleksey V. Zimin, Arthur L. Delcher, Liliana D Florea, David R. Kelley, Michael C. Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P. Van Tassell, Tad S. Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A. Yorke, Steven L Salzberg

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article numberR42
JournalGenome Biology
Volume10
Issue number4
DOIs
StatePublished - Apr 24 2009
Externally publishedYes

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genome assembly
genome
Genome
Synteny
cows
cattle
chromosome
Y Chromosome
Firearms
Human Genome
Base Pairing
Y chromosome
Nucleotides
Chromosomes
translocation
sequence analysis
nucleotides
chromosomes
methodology

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

A whole-genome assembly of the domestic cow, Bos taurus. / Zimin, Aleksey V.; Delcher, Arthur L.; Florea, Liliana D; 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.

In: Genome Biology, Vol. 10, No. 4, R42, 24.04.2009.

Research output: Contribution to journalArticle

Zimin, AV, Delcher, AL, Florea, LD, Kelley, DR, Schatz, MC, Puiu, D, Hanrahan, F, Pertea, G, Van Tassell, CP, Sonstegard, TS, Marçais, G, Roberts, M, Subramanian, P, Yorke, JA & Salzberg, SL 2009, 'A whole-genome assembly of the domestic cow, Bos taurus', Genome Biology, vol. 10, no. 4, R42. https://doi.org/10.1186/gb-2009-10-4-r42
Zimin AV, Delcher AL, Florea LD, Kelley DR, Schatz MC, Puiu D et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 2009 Apr 24;10(4). R42. https://doi.org/10.1186/gb-2009-10-4-r42
Zimin, Aleksey V. ; Delcher, Arthur L. ; Florea, Liliana D ; 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. / A whole-genome assembly of the domestic cow, Bos taurus. In: Genome Biology. 2009 ; Vol. 10, No. 4.
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