title: Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications.
abstract: BACKGROUND
  The ~17 Gb hexaploid bread wheat genome is a high priority and a major technical challenge for genomic studies. In particular, the D sub-genome is relatively lacking in genetic diversity, making it both difficult to map genetically, and a target for introgression of agriculturally useful traits. Elucidating its sequence and structure will therefore facilitate wheat breeding and crop improvement.
  
  
  RESULTS
  We generated shotgun sequences from each arm of flow-sorted Triticum aestivum chromosome 5D using 454 FLX Titanium technology, giving 1.34× and 1.61× coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. By a combination of sequence similarity and assembly-based methods, ~74% of the sequence reads were classified as repetitive elements, and coding sequence models of 1314 (5DS) and 2975 (5DL) genes were generated. The order of conserved genes in syntenic regions of previously sequenced grass genomes were integrated with physical and genetic map positions of 518 wheat markers to establish a virtual gene order for chromosome 5D.
  
  
  CONCLUSIONS
  The virtual gene order revealed a large-scale chromosomal rearrangement in the peri-centromeric region of 5DL, and a concentration of non-syntenic genes in the telomeric region of 5DS. Although our data support the large-scale conservation of Triticeae chromosome structure, they also suggest that some regions are evolving rapidly through frequent gene duplications and translocations.
  EBI European Nucleotide Archive, Study no. ERP002330.
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Lucas
authors.forename: Bala Anı
authors.initials: BA
authors.lastname: Akpınar
authors.forename: Hana
authors.initials: H
authors.lastname: Šimková
authors.forename: Marie
authors.initials: M
authors.lastname: Kubaláková
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.affiliation: Faculty of Engineering and Natural Sciences, Sabanci University, Orhanlı, 34956 Tuzla, Istanbul, Turkey. budak@sabanciuniv.edu.
authors.forename: Hikmet
authors.initials: H
authors.lastname: Budak
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D019295:Computational Biology; D066264:Datasets as Topic; D019143:Evolution, Molecular; D020440:Gene Duplication; D015321:Gene Rearrangement; D056726:Genetic Association Studies; D008040:Genetic Linkage; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D006109:Poaceae; D012343:RNA, Transfer / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D014178:Translocation, Genetic; D014908:Triticum / Q000235:genetics*
chemical_list: D012343:RNA, Transfer