title: A clone-free, single molecule map of the domestic cow (Bos taurus) genome.
abstract: BACKGROUND
  The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation.
  
  
  RESULTS
  The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts).
  
  
  CONCLUSIONS
  Alignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI's current designation of UMD3.1 sequence assembly as the "reference assembly" and the Btau4.6 as the "alternate assembly." The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds.
authors: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA. szhou@wisc.edu.
authors: Shiguo
authors: S
authors: Zhou
authors: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA. sgoldstein@wisc.edu.
authors: Steve
authors: S
authors: Goldstein
authors: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA. mplace@wisc.edu.
authors: Michael
authors: M
authors: Place
authors: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA. mcbechner@wisc.edu.
authors: Michael
authors: M
authors: Bechner
authors: Departamento de Materiales, Facultad de Minas, Universidad Nacional de Colombia, Sede Medellin, Calle 75 # 79A-51, Bloque M17, Medellin, Colombia, SA. dipaco@gmail.com.
authors: Diego
authors: D
authors: Patino
authors: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA. kpotamousis@wisc.edu.
authors: Konstantinos
authors: K
authors: Potamousis
authors: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA. praburavindran@gmail.com.
authors: Prabu
authors: P
authors: Ravindran
authors: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA. lpape@wisc.edu.
authors: Louise
authors: L
authors: Pape
authors: Department of Animal Science, University of California-Davis, Davis, CA, 95616, USA. gonzalo.rincon@zoetis.com.
authors: Gonzalo
authors: G
authors: Rincon
authors: Departamento de Materiales, Facultad de Minas, Universidad Nacional de Colombia, Sede Medellin, Calle 75 # 79A-51, Bloque M17, Medellin, Colombia, SA. jphernandezo@unal.edu.co.
authors: Juan
authors: J
authors: Hernandez-Ortiz
authors: Department of Animal Science, University of California-Davis, Davis, CA, 95616, USA. jfmedrano@ucdavis.edu.
authors: Juan F
authors: JF
authors: Medrano
authors: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA. dcschwartz@wisc.edu.
authors: David C
authors: DC
authors: Schwartz
mesh_terms: D000818:Animals; D002417:Cattle; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods; D066264:Datasets as Topic; D023061:Gene Order; D016678:Genome; D023281:Genomics / Q000379:methods