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Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture

Part of the Methods in Molecular Biology book series (MIMB,volume 2250)

Abstract

Transposable elements (TEs) are repetitive DNA sequences that have the ability to mobilize in the genome and create major effect mutations. Despite the importance of transposition as a source of genetic novelty, we still know little about the rate, landscape, and consequences of TE mobilization. This situation stems in large part from the repetitive nature of TEs, which complicates their analysis. Moreover, TE mobilization is typically rare and therefore new TE (i.e., non-reference) insertions tend to be missed in small-scale population studies. This chapter describes a TE-sequence capture approach designed to identify transposition events for most of the TE families that are potentially active in Arabidopsis thaliana. We show that our TE-sequence capture design provides an efficient means to detect with high sensitivity and specificity insertions that are present at a frequency as low as 1/1000 within a DNA sample.

Key words

  • Arabidopsis
  • Transposable elements
  • Transposition
  • Sequence capture

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Acknowledgments

We thank members of the Colot group for discussions, especially P. Baduel for critical reading of the manuscript. Support was from the Agence National de la Recherche (ANR-09-BLAN-0237, the Investissements d’Avenir ANR-10-LABX-54 MEMO LIFE, ANR-11-IDEX-0001-02 PSL* Research University to V.C) and the Centre National de la Recherche Scientifique (MOMENTUM program, to L.Q.).

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Correspondence to Leandro Quadrana or Vincent Colot .

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1 Electronic Supplementary Material

Supplementary Table 1

Identity of TE sequences included in the TE-sequence capture design (XLSX 20 kb)

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Quadrana, L., Silveira, A.B., Caillieux, E., Colot, V. (2021). Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture. In: Cho, J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1134-0_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1133-3

  • Online ISBN: 978-1-0716-1134-0

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