title: A whole-genome assembly of the domestic cow, Bos taurus.
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.
authors.affiliation: Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: Aleksey V
authors.initials: AV
authors.lastname: Zimin
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Delcher
authors.forename: Liliana
authors.initials: L
authors.lastname: Florea
authors.forename: David R
authors.initials: DR
authors.lastname: Kelley
authors.forename: Michael C
authors.initials: MC
authors.lastname: Schatz
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: Finnian
authors.initials: F
authors.lastname: Hanrahan
authors.forename: Geo
authors.initials: G
authors.lastname: Pertea
authors.forename: Curtis P
authors.initials: CP
authors.lastname: Van Tassell
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.forename: Guillaume
authors.initials: G
authors.lastname: Marçais
authors.forename: Michael
authors.initials: M
authors.lastname: Roberts
authors.forename: Poorani
authors.initials: P
authors.lastname: Subramanian
authors.forename: James A
authors.initials: JA
authors.lastname: Yorke
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping; D005260:Female; D016678:Genome / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D023281:Genomics; D006801:Humans; D008297:Male; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data; D026801:Synteny; D014998:Y Chromosome / Q000235:genetics