Plant Transposable Elements pp 41-58

Part of the Topics in Current Genetics book series (TCG, volume 24) | Cite as

Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content

  • Concepcion Muñoz-Diez
  • Clémentine Vitte
  • Jeffrey Ross-Ibarra
  • Brandon S. Gaut
  • Maud I. Tenaillon
Chapter

Abstract

Transposable element (TE) content explains a large part of Eukaryotic genome size variation. TE content is determined by transposition, removal and host responses, but the efficiency of these forces is ultimately governed by genetic drift and natural selection. Contribution of TE families to genome size variation has been recently quantified using next generation sequencing (NGS) in two species pairs: Zea mays ssp. mays and Zea luxurians, Arabidopsis lyrata and A. thaliana. In both interspecific comparisons, genome-wide differences in TE content rather than the proliferation of a small subset of TE families was observed. We discuss three nonexclusive hypotheses to explain this pattern: selection for genome shrinkage, differential efficiency of epigenetic control, and a purely stochastic process of genome size evolution. Additional genome-wide assessments are needed to assess the extent to which selection shapes TE genomic content. To facilitate such studies, we discuss the use of NGS in “orphan” species.

Keywords

Repetitive DNA Selection Genome shrinkage Effective population size Epigenetic control Maize Arabidopsis 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Concepcion Muñoz-Diez
    • 1
  • Clémentine Vitte
    • 2
  • Jeffrey Ross-Ibarra
    • 3
  • Brandon S. Gaut
    • 1
  • Maud I. Tenaillon
    • 2
  1. 1.Department of Ecology and Evolutionary BiologyUC IrvineIrvineUSA
  2. 2.CNRS, UMR 0320 / UMR 8120 Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParisTechGif-sur-YvetteFrance
  3. 3.The Department of Plant Sciences and The Genome Center and Center for Population BiologyUC DavisDavisUSA

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