title: Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).
abstract: Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland OT, Gatersleben, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Mascher
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Muehlbauer
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
authors.forename: Jarrod
authors.initials: J
authors.lastname: Chapman
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.forename: María
authors.initials: M
authors.lastname: Muñoz-Amatriaín
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Close
authors.forename: Roger P
authors.initials: RP
authors.lastname: Wise
authors.forename: Alan H
authors.initials: AH
authors.lastname: Schulman
authors.forename: Axel
authors.initials: A
authors.lastname: Himmelbach
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.forename: Jesse A
authors.initials: JA
authors.lastname: Poland
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
mesh_terms: D020451:Contig Mapping / Q000379:methods*; D005828:Genetics, Population; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D001467:Hordeum / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: Hordeum vulgare; barley; genetic mapping; genome assembly; next-generation sequencing; population sequencing; technical advance