Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage
Creators
- 1. Max Planck Institute for Developmental Biology
- 2. The Leibniz Institute of Plant Genetics and Crop Plant Research
- 3. Max Planck Institute for Plant Breeding Research
- 4. University of Chicago
Description
There has been much excitement about the possibility that exposure to specific environments can induce an ecological memory in the form of whole-sale, genome-wide epigenetic changes that are maintained over many generations. In the model plant Arabidopsis thaliana, numerous heritable DNA methylation differences have been identified in greenhouse-grown isogenic lines, but it remains unknown how natural, highly variable environments affect the rate and spectrum of such changes. Here we present detailed methylome analyses in a geographically dispersed A. thaliana population that constitutes a collection of near-isogenic lines, diverged for at least a century from a common ancestor. Methylome variation largely reflected genetic distance, and was in many aspects similar to that of lines raised in uniform conditions. Thus, even when plants are grown in varying and diverse natural sites, genome-wide epigenetic variation accumulates mostly in a clock-like manner, and epigenetic divergence thus parallels the pattern of genome-wide DNA sequence divergence.
Data availability
The authors confirm that all data underlying the findings are fully available without restriction. The DNA and RNA sequencing data have been deposited at the European Nucleotide Archive under accession numbers PRJEB5287 and PRJEB5331. A GBrowse instance for DNA methylation and transcriptome data is available at http://gbrowse.weigelworld.org/fgb2/gbrowse/ath_methyl_haplotype1/. DNA methylation data, MR coordinates and genetic variant information have also been uploaded to the genome browser of the EPIC consortium (http://genomevolution.org/r/939v).Files
journal.pgen.1004920.pdf
Files
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Additional details
Identifiers
- DOI
- 10.1371/journal.pgen.1004920
- Other
- oai:uchicago.tind.io:10233
Related works
- Cites
- https://doi.org/10.1101/009225 (URL)
Funding
- European Commission
- Marie Curie FP7 fellowship
- National Institutes of Health
- GM083068
- European Commission
- AENEAS
- Deutsche Forschungsgemeinschaft
- Gottfried Wilhelm Leibniz Award
- Max Planck Society