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Detecting Signatures of TE Polymorphisms in Short-Read Sequencing Data

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

Abstract

Transposable elements (TEs) are an important cause of evolutionary change and functional diversity, yet they are routinely discarded in the first steps of many analyses. In this chapter we show how, given a reference genome, TEs can be incorporated fairly easily into functional and evolutionary studies. We offer a glimpse into a program which detects TE insertion polymorphisms and discuss practical issues arising from the diversity of TEs and genome architectures. Detecting TE polymorphisms relies on a series of ad hoc criteria because, in contrast to single nucleotide polymorphisms, there is no general way to model TE activity. Signatures of TE polymorphisms in reference-aligned reads depend on the type of TE as well as on the complexity of the genomic background. As a consequence, a basic understanding of the limitations imposed by the data and of what the algorithm is doing is important to obtain reliable results. Here, we hope to convey such a basic understanding and help researchers to avoid some of the common pitfalls of TE polymorphism detection.

Key words

  • Detettore
  • Discordant read pairs
  • Functional genomics
  • Population genomics
  • Short-read sequencing
  • Split reads
  • Transposable element polymorphisms

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Acknowledgments

This work was supported by the Swiss National Science Foundation (PZ00P3_154724) and the University Research Priority Programs (URPP) Evolution in Action of the University of Zürich.

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Correspondence to Anne C. Roulin .

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Stritt, C., Roulin, A.C. (2021). Detecting Signatures of TE Polymorphisms in 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_17

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_17

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