title: Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes.
abstract: OBJECTIVE
  Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots.
  
  
  METHODS
  To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons.
  
  
  RESULTS
  The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4-5 % (asparagus) or 3-4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize.
  
  
  CONCLUSIONS
  Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.
authors.affiliation: CNRS, UMR de Génétique Végétale, Ferme du Moulon, F-91190 Gif sur Yvette, France. vitte@moulon.inra.fr
authors.forename: C
authors.initials: C
authors.lastname: Vitte
authors.forename: M C
authors.initials: MC
authors.lastname: Estep
authors.forename: J
authors.initials: J
authors.lastname: Leebens-Mack
authors.forename: J L
authors.initials: JL
authors.lastname: Bennetzen
mesh_terms: D027761:Asparagus Plant / Q000235:genetics*; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D016000:Cluster Analysis; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D019697:Onions / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences / Q000235:genetics*
chemical_list: D018626:Retroelements
keywords: Allium cepa; Asparagales; Asparagus officinalis; BAC annotation; LTR retrotransposons; garden asparagus; onion; transposable elements