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Detecting Horizontal Transfer of Transposons

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Transposable Elements

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2607))

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Abstract

Transposable elements (TEs) are prevalent genomic components which can replicate as a function of mobilization in eukaryotes. Not only do they alter genome structure, they also play regulatory functions or organize chromatin structure. In addition to vertical parent-to-offspring inheritance, TEs can also horizontally “jump” between species, known as horizontal transposon transfer (HTT). This can rapidly alter the course of genome evolution. In this chapter, we provide a practical framework to detect HTT events. Our HTT detection framework is based on the use of sequence alignment to determine the divergence/conservation profiles of TE families to determine the history of expansion events. In summary, it includes (a) workflow of HTT detection from Ab initio identified TEs; (b) workflow for detecting HTT for specific, curated TEs; and (c) workflow for validating detected HTT candidates. Our framework covers two common scenarios of HTT detection in the modern omics era, and we believe it will serve as a valuable toolbox for the TE and genomics research community.

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Author information

Author notes

  1. James D. Galbraith and Atma M. Ivancevic contributed equally to this work.

Authors and Affiliations

  1. Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall, UK

    James D. Galbraith

  2. Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA

    Atma M. Ivancevic

  3. School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia

    Zhipeng Qu & David L. Adelson

  4. South Australian Museum, Adelaide, SA, Australia

    David L. Adelson

Authors
  1. James D. Galbraith
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  2. Atma M. Ivancevic
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  3. Zhipeng Qu
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  4. David L. Adelson
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Corresponding author

Correspondence to David L. Adelson .

Editor information

Editors and Affiliations

  1. Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK

    Miguel R. Branco

  2. School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK

    Alexandre de Mendoza Soler

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Galbraith, J.D., Ivancevic, A.M., Qu, Z., Adelson, D.L. (2023). Detecting Horizontal Transfer of Transposons. In: Branco, M.R., de Mendoza Soler, A. (eds) Transposable Elements. Methods in Molecular Biology, vol 2607. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2883-6_3

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  • DOI: https://doi.org/10.1007/978-1-0716-2883-6_3

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2882-9

  • Online ISBN: 978-1-0716-2883-6

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