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Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data

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

Abstract

Transposable elements (TEs) are powerful generators of major-effect mutations, most of which are deleterious at the species level and maintained at very low frequencies within populations. As reference genomes can only capture a minor fraction of such variants, methods were developed to detect TE insertion polymorphisms (TIPs) in non-reference genomes from the short-read sequencing data that are becoming increasingly available. We present here a bioinformatic framework combining an improved version of the SPLITREADER and TEPID pipelines to detect non-reference TE presence and reference TE absence variants, respectively. We benchmark our method on ten non-reference Arabidopsis thaliana genomes and demonstrate its high specificity and sensitivity in the detection of TIPs between genomes.

Key words

  • Transposable element
  • TE insertion polymorphism

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  • DOI: 10.1007/978-1-0716-1134-0_15
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References

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Acknowledgments

We thank members of the Colot group for discussions. P.B. was the recipient of a postdoctoral fellowship (code SPF20170938626) from the Fondation pour la Recherche Médicale (FRM). 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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Baduel, P., Quadrana, L., Colot, V. (2021). Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data. 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_15

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_15

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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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