title: Bos taurus genome assembly.
abstract: BACKGROUND
  We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque.
  
  
  RESULTS
  The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information.Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly.
  
  
  CONCLUSIONS
  The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research.
authors.affiliation: Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Yue
authors.initials: Y
authors.lastname: Liu
authors.forename: Xiang
authors.initials: X
authors.lastname: Qin
authors.forename: Xing-Zhi Henry
authors.initials: XZ
authors.lastname: Song
authors.forename: Huaiyang
authors.initials: H
authors.lastname: Jiang
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Shen
authors.forename: K James
authors.initials: KJ
authors.lastname: Durbin
authors.forename: Sigbjørn
authors.initials: S
authors.lastname: Lien
authors.forename: Matthew Peter
authors.initials: MP
authors.lastname: Kent
authors.forename: Marte
authors.initials: M
authors.lastname: Sodeland
authors.forename: Yanru
authors.initials: Y
authors.lastname: Ren
authors.forename: Lan
authors.initials: L
authors.lastname: Zhang
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.forename: Paul
authors.initials: P
authors.lastname: Havlak
authors.forename: Kim C
authors.initials: KC
authors.lastname: Worley
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D005819:Genetic Markers; D016678:Genome; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers