title: Unlocking the barley genome by chromosomal and comparative genomics.
abstract: We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
authors.affiliation: Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Mihaela
authors.initials: M
authors.lastname: Martis
authors.forename: Pete E
authors.initials: PE
authors.lastname: Hedley
authors.forename: Hana
authors.initials: H
authors.lastname: Simková
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.forename: Jenny A
authors.initials: JA
authors.lastname: Morris
authors.forename: Burkhard
authors.initials: B
authors.lastname: Steuernagel
authors.forename: Stefan
authors.initials: S
authors.lastname: Taudien
authors.forename: Stephan
authors.initials: S
authors.lastname: Roessner
authors.forename: Heidrun
authors.initials: H
authors.lastname: Gundlach
authors.forename: Marie
authors.initials: M
authors.lastname: Kubaláková
authors.forename: Pavla
authors.initials: P
authors.lastname: Suchánková
authors.forename: Florent
authors.initials: F
authors.lastname: Murat
authors.forename: Marius
authors.initials: M
authors.lastname: Felder
authors.forename: Thomas
authors.initials: T
authors.lastname: Nussbaumer
authors.forename: Andreas
authors.initials: A
authors.lastname: Graner
authors.forename: Jerome
authors.initials: J
authors.lastname: Salse
authors.forename: Takashi
authors.initials: T
authors.lastname: Endo
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Sato
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Dolezel
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
mesh_terms: D002503:Centromere / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D023061:Gene Order / Q000235:genetics; D015321:Gene Rearrangement / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D001467:Hordeum / Q000235:genetics*; D008957:Models, Genetic; D012275:Oryza / Q000235:genetics; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics