title: Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.
abstract: BACKGROUND
  The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome.
  
  
  RESULTS
  TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea.
  
  
  CONCLUSIONS
  This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.
authors.affiliation: Unité Mixte de Recherche de l'Institut National de la Recherche Agronomique, Lorraine Université Interactions Arbres/Microorganismes, Centre de Nancy, Champenoux, France. labbejj@ornl.gov
authors.forename: Jessy
authors.initials: J
authors.lastname: Labbé
authors.forename: Claude
authors.initials: C
authors.lastname: Murat
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Morin
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
authors.forename: François
authors.initials: F
authors.lastname: Le Tacon
authors.forename: Francis
authors.initials: F
authors.lastname: Martin
mesh_terms: D004271:DNA, Fungal / Q000235:genetics*; D019143:Evolution, Molecular; D016681:Genome, Fungal / Q000502:physiology*; D055399:Laccaria / Q000235:genetics*; D038821:Mycorrhizae / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*
chemical_list: D004271:DNA, Fungal; D018626:Retroelements