Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021:2250:157-169.
doi: 10.1007/978-1-0716-1134-0_15.

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

Pierre Baduel  1 , Leandro Quadrana  2 , Vincent Colot  3
Affiliations

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

Pierre Baduel et al. Methods Mol Biol. 2021.

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.

Keywords: TE insertion polymorphism; Transposable element.

PubMed Disclaimer

References

    1. Quadrana L et al (2016) The Arabidopsis thaliana mobilome and its impact at the species level. eLife 5:e15716 - DOI
    1. Stuart T et al (2016) Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. eLife 5:e20777 - DOI
    1. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359 - DOI
    1. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842 - DOI
    1. Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079 - DOI

Publication types

Substances

LinkOut - more resources