title: Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces.
abstract: To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.
authors.affiliation: Institut National de la Recherche Agronomique, Université Blaise Pascal, Unité Mixte de Recherche 1095 Genetics Diversity and Ecophysiology of Cereals, F-63100 Clermont-Ferrand, France. frederic.choulet@clermont.inra.fr
authors.forename: Frédéric
authors.initials: F
authors.lastname: Choulet
authors.forename: Thomas
authors.initials: T
authors.lastname: Wicker
authors.forename: Camille
authors.initials: C
authors.lastname: Rustenholz
authors.forename: Etienne
authors.initials: E
authors.lastname: Paux
authors.forename: Jérome
authors.initials: J
authors.lastname: Salse
authors.forename: Philippe
authors.initials: P
authors.lastname: Leroy
authors.forename: Stéphane
authors.initials: S
authors.lastname: Schlub
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Le Paslier
authors.forename: Ghislaine
authors.initials: G
authors.lastname: Magdelenat
authors.forename: Catherine
authors.initials: C
authors.lastname: Gonthier
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.forename: Hikmet
authors.initials: H
authors.lastname: Budak
authors.forename: James
authors.initials: J
authors.lastname: Breen
authors.forename: Michael
authors.initials: M
authors.lastname: Pumphrey
authors.forename: Sixin
authors.initials: S
authors.lastname: Liu
authors.forename: Xiuying
authors.initials: X
authors.lastname: Kong
authors.forename: Jizeng
authors.initials: J
authors.lastname: Jia
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
authors.forename: James A
authors.initials: JA
authors.lastname: Anderson
authors.forename: Bikram S
authors.initials: BS
authors.lastname: Gill
authors.forename: Rudi
authors.initials: R
authors.lastname: Appels
authors.forename: Beat
authors.initials: B
authors.lastname: Keller
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
mesh_terms: D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant; D020451:Contig Mapping; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D017422:Sequence Analysis, DNA; D016615:Telomere / Q000235:genetics; D014908:Triticum / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant