title: Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
abstract: White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20,356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.
  
  
  BACKGROUND
  The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada. ibirol@bcgsc.ca
authors.forename: Inanc
authors.initials: I
authors.lastname: Birol
authors.forename: Anthony
authors.initials: A
authors.lastname: Raymond
authors.forename: Shaun D
authors.initials: SD
authors.lastname: Jackman
authors.forename: Stephen
authors.initials: S
authors.lastname: Pleasance
authors.forename: Robin
authors.initials: R
authors.lastname: Coope
authors.forename: Greg A
authors.initials: GA
authors.lastname: Taylor
authors.forename: Macaire Man Saint
authors.initials: MM
authors.lastname: Yuen
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Keeling
authors.forename: Dana
authors.initials: D
authors.lastname: Brand
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Vandervalk
authors.forename: Heather
authors.initials: H
authors.lastname: Kirk
authors.forename: Pawan
authors.initials: P
authors.lastname: Pandoh
authors.forename: Richard A
authors.initials: RA
authors.lastname: Moore
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Zhao
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Mungall
authors.forename: Barry
authors.initials: B
authors.lastname: Jaquish
authors.forename: Alvin
authors.initials: A
authors.lastname: Yanchuk
authors.forename: Carol
authors.initials: C
authors.lastname: Ritland
authors.forename: Brian
authors.initials: B
authors.lastname: Boyle
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
authors.forename: Kermit
authors.initials: K
authors.lastname: Ritland
authors.forename: John
authors.initials: J
authors.lastname: Mackay
authors.forename: Jörg
authors.initials: J
authors.lastname: Bohlmann
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
mesh_terms: D001483:Base Sequence; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D028222:Picea / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software