title: A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.
abstract: The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616, USA.
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
authors.forename: Frank M
authors.initials: FM
authors.lastname: You
authors.forename: Karin R
authors.initials: KR
authors.lastname: Deal
authors.forename: Yaqin
authors.initials: Y
authors.lastname: Ma
authors.forename: Yuqin
authors.initials: Y
authors.lastname: Hu
authors.forename: Naxin
authors.initials: N
authors.lastname: Huo
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.forename: Jirui
authors.initials: J
authors.lastname: Wang
authors.forename: Shiyong
authors.initials: S
authors.lastname: Chen
authors.forename: Chad M
authors.initials: CM
authors.lastname: Jorgensen
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Patrick E
authors.initials: PE
authors.lastname: McGuire
authors.forename: Shiran
authors.initials: S
authors.lastname: Pasternak
authors.forename: Joshua C
authors.initials: JC
authors.lastname: Stein
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
authors.forename: Melissa
authors.initials: M
authors.lastname: Kramer
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Shahryar F
authors.initials: SF
authors.lastname: Kianian
authors.forename: Mihaela M
authors.initials: MM
authors.lastname: Martis
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Sunish K
authors.initials: SK
authors.lastname: Sehgal
authors.forename: Wanlong
authors.initials: W
authors.lastname: Li
authors.forename: Bikram S
authors.initials: BS
authors.lastname: Gill
authors.forename: Michael W
authors.initials: MW
authors.lastname: Bevan
authors.forename: Hana
authors.initials: H
authors.lastname: Simková
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Dolezel
authors.forename: Song
authors.initials: S
authors.lastname: Weining
authors.forename: Gerard R
authors.initials: GR
authors.lastname: Lazo
authors.forename: Olin D
authors.initials: OD
authors.lastname: Anderson
authors.forename: Jan
authors.initials: J
authors.lastname: Dvorak
mesh_terms: D002503:Centromere / Q000648:ultrastructure; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000648:ultrastructure; D020451:Contig Mapping; D019143:Evolution, Molecular; D017343:Genes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D006109:Poaceae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics
chemical_list: D005819:Genetic Markers
keywords: BAC contig coassembly; Oryza; gene density; single nucleotide polymorphism; synteny