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Plant Transposable Elements pp 87–93Cite as

Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq

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

Abstract

Active transposable elements (TEs) generate insertion polymorphisms that can be detected through genome resequencing strategies. However, these techniques may have limitations for organisms with large genomes or for somatic insertions. Here, we present a method that takes advantage of the extrachromosomal circular DNA (eccDNA) forms of actively transposing TEs in order to detect and characterize active TEs in any plant or animal tissue. Mobilome-seq consists in selectively amplifying and sequencing eccDNAs. It relies on linear digestion of genomic DNA followed by rolling circle amplification of circular DNA. Both active DNA transposons and retrotransposons can be identified using this technique.

Key words

  • Extrachromosomal circular DNA (eccDNA)
  • Plasmid safe
  • Rolling circle DNA amplification (RCA)
  • Phi29
  • Transposable elements (TEs)
  • Retrotransposons
  • Mobilome sequencing

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Acknowledgments

This work was funded by IRD, a French ANR grant (ANR-13-JSV6-0002 “ExtraChrom”) and a EU Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 764965 (“EpiDiverse”) to M.M.

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Authors and Affiliations

  1. IRD, UMR232 DIADE, University of Montpellier, Montpellier, France

    Sophie Lanciano, Panpan Zhang & Marie Mirouze

  2. Laboratory of Plant Genome and Development, CNRS, University of Perpignan, Perpignan, France

    Sophie Lanciano, Panpan Zhang, Christel Llauro & Marie Mirouze

  3. University Cote d’Azur, Inserm, CNRS, IRCAN, Nice, France

    Sophie Lanciano

Authors
  1. Sophie Lanciano
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  2. Panpan Zhang
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  3. Christel Llauro
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  4. Marie Mirouze
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Corresponding author

Correspondence to Marie Mirouze .

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Editors and Affiliations

  1. CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai, China

    Dr. Jungnam Cho

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Lanciano, S., Zhang, P., Llauro, C., Mirouze, M. (2021). Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq. 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_7

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_7

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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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