Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity

SR Eichten, T Stuart, A Srivastava, R Lister, JO Borevitz
doi: https://doi.org/10.1101/039602
SR Eichten
1ARC Centre of Excellence in Plant Energy Biology. The Australian National University, Canberra, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
T Stuart
2ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
A Srivastava
2ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
R Lister
2ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
JO Borevitz
1ARC Centre of Excellence in Plant Energy Biology. The Australian National University, Canberra, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: justin.borevitz@anu.edu.au
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon. Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertion or deletions are associated with nearby differential methylation. This study highlights the importance of genetic variation when assessing DNA methylation variation between samples and provides a valuable map of DNA methylation across diverse re-sequenced accessions of this model cereal species.

Reviewer Link to deposited data All data is publicly available in the NCBI short read archive under BioProject PRJNA281014. Data tables are available for download at https://drive.google.com/file/d/0BzBxfoxlBCneNkY1TFJDU29iSUU/view?usp=sharing

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted February 17, 2016.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity
SR Eichten, T Stuart, A Srivastava, R Lister, JO Borevitz
bioRxiv 039602; doi: https://doi.org/10.1101/039602
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity
SR Eichten, T Stuart, A Srivastava, R Lister, JO Borevitz
bioRxiv 039602; doi: https://doi.org/10.1101/039602

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (2428)
  • Biochemistry (4784)
  • Bioengineering (3328)
  • Bioinformatics (14657)
  • Biophysics (6630)
  • Cancer Biology (5163)
  • Cell Biology (7417)
  • Clinical Trials (138)
  • Developmental Biology (4357)
  • Ecology (6869)
  • Epidemiology (2057)
  • Evolutionary Biology (9905)
  • Genetics (7341)
  • Genomics (9510)
  • Immunology (4545)
  • Microbiology (12658)
  • Molecular Biology (4937)
  • Neuroscience (28285)
  • Paleontology (199)
  • Pathology (804)
  • Pharmacology and Toxicology (1388)
  • Physiology (2019)
  • Plant Biology (4487)
  • Scientific Communication and Education (977)
  • Synthetic Biology (1297)
  • Systems Biology (3909)
  • Zoology (725)