title: Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.
abstract: BACKGROUND
  The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.
  
  
  RESULTS
  We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome.
  
  
  CONCLUSIONS
  In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.
authors.forename: David B
authors.initials: DB
authors.lastname: Neale
authors.forename: Jill L
authors.initials: JL
authors.lastname: Wegrzyn
authors.forename: Kristian A
authors.initials: KA
authors.lastname: Stevens
authors.forename: Aleksey V
authors.initials: AV
authors.lastname: Zimin
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: Marc W
authors.initials: MW
authors.lastname: Crepeau
authors.forename: Charis
authors.initials: C
authors.lastname: Cardeno
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authors.lastname: Koriabine
authors.forename: Ann E
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authors.lastname: Holtz-Morris
authors.forename: John D
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authors.lastname: Liechty
authors.forename: Pedro J
authors.initials: PJ
authors.lastname: Martínez-García
authors.forename: Hans A
authors.initials: HA
authors.lastname: Vasquez-Gross
authors.forename: Brian Y
authors.initials: BY
authors.lastname: Lin
authors.forename: Jacob J
authors.initials: JJ
authors.lastname: Zieve
authors.forename: William M
authors.initials: WM
authors.lastname: Dougherty
authors.forename: Sara
authors.initials: S
authors.lastname: Fuentes-Soriano
authors.forename: Le-Shin
authors.initials: LS
authors.lastname: Wu
authors.forename: Don
authors.initials: D
authors.lastname: Gilbert
authors.forename: Guillaume
authors.initials: G
authors.lastname: Marçais
authors.forename: Michael
authors.initials: M
authors.lastname: Roberts
authors.forename: Carson
authors.initials: C
authors.lastname: Holt
authors.forename: Mark
authors.initials: M
authors.lastname: Yandell
authors.forename: John M
authors.initials: JM
authors.lastname: Davis
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Smith
authors.forename: Jeffrey F D
authors.initials: JF
authors.lastname: Dean
authors.forename: W Walter
authors.initials: WW
authors.lastname: Lorenz
authors.forename: Ross W
authors.initials: RW
authors.lastname: Whetten
authors.forename: Ronald
authors.initials: R
authors.lastname: Sederoff
authors.forename: Nicholas
authors.initials: N
authors.lastname: Wheeler
authors.forename: Patrick E
authors.initials: PE
authors.lastname: McGuire
authors.forename: Doreen
authors.initials: D
authors.lastname: Main
authors.forename: Carol A
authors.initials: CA
authors.lastname: Loopstra
authors.forename: Keithanne
authors.initials: K
authors.lastname: Mockaitis
authors.forename: Pieter J
authors.initials: PJ
authors.lastname: deJong
authors.forename: James A
authors.initials: JA
authors.lastname: Yorke
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Charles H
authors.initials: CH
authors.lastname: Langley
mesh_terms: D020451:Contig Mapping / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D006238:Haploidy; D041603:Pinus taeda / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018744:DNA, Plant