title: Organization and evolution of transposable  elements along the bread wheat chromosome 3B.
abstract: BACKGROUND
  The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far.
  
  
  RESULTS
  We develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation.
  
  
  CONCLUSIONS
  Accurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.
authors.forename: Josquin
authors.initials: J
authors.lastname: Daron
authors.forename: Natasha
authors.initials: N
authors.lastname: Glover
authors.forename: Lise
authors.initials: L
authors.lastname: Pingault
authors.forename: Sébastien
authors.initials: S
authors.lastname: Theil
authors.forename: Véronique
authors.initials: V
authors.lastname: Jamilloux
authors.forename: Etienne
authors.initials: E
authors.lastname: Paux
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.forename: Sophie
authors.initials: S
authors.lastname: Mangenot
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Hadi
authors.initials: H
authors.lastname: Quesneville
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
authors.forename: Frédéric
authors.initials: F
authors.lastname: Choulet
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D008957:Models, Genetic; D010802:Phylogeny; D012641:Selection, Genetic; D014908:Triticum / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements