title: Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.
abstract: BACKGROUND
  Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses.
  
  
  RESULTS
  Here, we systematically assessed the utility of paired-end and mate-pair (MP) next-generation sequencing libraries with insert sizes ranging from 170 bp to 25 kb, for genome coverage and for improving scaffolding of a mammalian genome (Rattus norvegicus). Despite a lower library complexity, large insert MP libraries (20 or 25 kb) provided very high physical genome coverage and were found to efficiently span repeat elements in the genome. Medium-sized (5, 8 or 15 kb) MP libraries were much more efficient for genome structure analysis than the more commonly used shorter insert paired-end and 3 kb MP libraries. Furthermore, the combination of medium- and large insert libraries resulted in a 3-fold increase in N50 in scaffolding processes. Finally, we show that our data can be used to evaluate and improve contig order and orientation in the current rat reference genome assembly.
  
  
  CONCLUSIONS
  We conclude that applying combinations of mate-pair libraries with insert sizes that match the distributions of repetitive elements improves contig scaffolding and can contribute to the finishing of draft genomes.
authors.affiliation: Hubrecht Institute/KNAW and University Medical Center Utrecht, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands.
authors.forename: Sebastiaan
authors.initials: S
authors.lastname: van Heesch
authors.forename: Wigard P
authors.initials: WP
authors.lastname: Kloosterman
authors.forename: Nico
authors.initials: N
authors.lastname: Lansu
authors.forename: Frans-Paul
authors.initials: FP
authors.lastname: Ruzius
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Levandowsky
authors.forename: Clarence C
authors.initials: CC
authors.lastname: Lee
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.forename: Steve
authors.initials: S
authors.lastname: Goldstein
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
authors.forename: Timothy T
authors.initials: TT
authors.lastname: Harkins
authors.forename: Victor
authors.initials: V
authors.lastname: Guryev
authors.forename: Edwin
authors.initials: E
authors.lastname: Cuppen
mesh_terms: D000818:Animals; D001483:Base Sequence; D020451:Contig Mapping / Q000379:methods; D015723:Gene Library; D016678:Genome; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D051381:Rats / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*