Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

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Data availability
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Abstract

Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.

Data availability

The following data sets were generated

1. Stuart T
2. Eichten SR
3. Cahn J
4. Karpievitch Y
5. Borevitz JO
6. Lister R
(2016) Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
Available at Dryad Digital Repository under a CC0 Public Domain Dedication.

http://dx.doi.org/10.5061/dryad.187b3

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http://www.ncbi.nlm.nih.gov/sra?term=SRA012474
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2. Schultz MD
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http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43858
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http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43857
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Article and author information

Author details

Tim Stuart

ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.
Steven Eichten

ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2268-395X
Jonathan Cahn

ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5006-741X
Yuliya Karpievitch

ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.
Justin Borevitz

ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia

Competing interests
The authors declare that no competing interests exist.
Ryan Lister

ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia

For correspondence
ryan.lister@uwa.edu.au

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-6637-7239

Funding

Centre of Excellence in Plant Energy Biology, Australian Research Council (CE140100008)

Tim Stuart
Steven Eichten
Jonathan Cahn
Yuliya Karpievitch
Justin Borevitz
Ryan Lister

Australian Research Council

Tim Stuart
Steven Eichten
Jonathan Cahn
Yuliya Karpievitch
Justin Borevitz
Ryan Lister

Sylvia and Charles Viertel Charitable Foundation

Ryan Lister

Australian Research Council (FT120100862)

Ryan Lister

Australian Research Council (DE150101206)

Steven Eichten

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.