, Volume 141, Issue 7–9, pp 369–379 | Cite as

Internal deletions of transposable elements: the case of Lemi elements

  • AbdelHakime Negoua
  • Jacques-Deric Rouault
  • Mohamed Chakir
  • Pierre Capy


Mobile elements using a “cut and paste” mechanism of transposition (Class II) are frequently prone to internal deletions and the question of the origin of these copies remains elusive. In this study, we looked for copies belonging to the Lemi Family (Tc1-mariner-IS630 SuperFamily) in the plant genomes, and copies within internal deletions were analyzed in detail. Lemi elements are found exclusively in Eudicots, and more than half of the copies have been deleted. All deletions occur between microhomologies (direct repeats from 2 to 13 bp). Copies less than 500 bp long, similar to MITEs, are frequent. These copies seem to result from large deletions occurring between microhomologies present within a region of 300 bp at both extremities of the element. These regions are particularly A/T rich, compared to the internal part of the element, which increases the probability of observing short direct repeats. Most of the molecular mechanisms responsible for double strand break repair are able to induce deletions between microhomologies during the repair process. This could be a quick way to reduce the population of active copies within a genome and, more generally, to reduce the overall activity of the element after it has entered a naive genome.


Transposable elements Lemi (Tc1-mariner-IS630Internal deletion Eudicots Mechanisms of repair Microhomologies 

Supplementary material

10709_2013_9736_MOESM1_ESM.pdf (57 kb)
Supplementary data - Figure 1: Phylogeny of Lemi copies belonging to the papilionis Tribe. The minimum size of the copies is 2,035 bp. The phylogeny was constructed using the Neighbor-Joining method (default parameters, bootstrap with 1,000 replications) of MEGA. (PDF 57 kb)
10709_2013_9736_MOESM2_ESM.pdf (464 kb)
Supplementary data – Figure 2: Dotplot of mariner and Lemi elements of M. truncaluta (MtLemi1) and A. thaliana (AtLemi1) against themselves using dotmatcher of EMBOSS. (PDF 464 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • AbdelHakime Negoua
    • 1
  • Jacques-Deric Rouault
    • 2
    • 3
  • Mohamed Chakir
    • 1
  • Pierre Capy
    • 2
    • 3
  1. 1.Laboratoire Aliment, Environnement et Santé, Faculté des Sciences et TechniquesUniversité Cadi AyyadMarrakechMorocco
  2. 2.Laboratoire Evolution, Génomes et SpéciationCNRSGif-sur-YvetteFrance
  3. 3.Université Paris-SudOrsay CedexFrance

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