title: Sequencing and assembly of the 22-gb loblolly pine genome.
abstract: Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun sequencing of a single megagametophyte, the haploid tissue of a single pine seed. Although that constrained the quantity of available DNA, the resulting haploid sequence data were well-suited for assembly. The haploid sequence was augmented with multiple linking long-fragment mate pair libraries from the parental diploid DNA. For the longest fragments, we used novel fosmid DiTag libraries. Sequences from the linking libraries that did not match the megagametophyte were identified and removed. Assembly of the sequence data were aided by condensing the enormous number of paired-end reads into a much smaller set of longer "super-reads," rendering subsequent assembly with an overlap-based assembly algorithm computationally feasible. To further improve the contiguity and biological utility of the genome sequence, additional scaffolding methods utilizing independent genome and transcriptome assemblies were implemented. The combination of these strategies resulted in a draft genome sequence of 20.15 billion bases, with an N50 scaffold size of 66.9 kbp.
authors.affiliation: Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Zimin
authors.forename: Kristian A
authors.initials: KA
authors.lastname: Stevens
authors.forename: Marc W
authors.initials: MW
authors.lastname: Crepeau
authors.forename: Ann
authors.initials: A
authors.lastname: Holtz-Morris
authors.forename: Maxim
authors.initials: M
authors.lastname: Koriabine
authors.forename: Guillaume
authors.initials: G
authors.lastname: Marçais
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: Michael
authors.initials: M
authors.lastname: Roberts
authors.forename: Jill L
authors.initials: JL
authors.lastname: Wegrzyn
authors.forename: Pieter J
authors.initials: PJ
authors.lastname: de Jong
authors.forename: David B
authors.initials: DB
authors.lastname: Neale
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: James A
authors.initials: JA
authors.lastname: Yorke
authors.forename: Charles H
authors.initials: CH
authors.lastname: Langley
mesh_terms: D018745:Genome, Plant; D023281:Genomics; D006238:Haploidy; D056771:Ovule / Q000235:genetics*; D041603:Pinus taeda / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
keywords: (see cocoa genome); Pinus taeda L.; conifer; de novo assembly; fosmid; genome; loblolly pine; placeholder