DOI: 10.5061/dryad.zs7h44j6r
title: Differentially methylated cytosines in Fragaria vesca

description: Epigenetic change is considered relatively unstable and short-lived,
 questioning its contribution to long-term adaptive potential. However,
 epigenetic modifications can accumulate in the presence of environmental
 stress, resulting in beneficial epigenetic memories where environments are
 challenging. Diverging epigenetic memories have been observed across large
 spatial scales, and can persist through multiple generations even in the
 absence of the causative environmental stressor. It is unknown, however,
 to what extent epigenetic variation contributes to fine-scale population
 structure and evolution. We compared DNA methylation patterns between a
 steep, altitudinal gradient (&lt;2 km) and a wide spatial gradient
 (&gt;500 km) using whole genome bisulfite sequencing data from 30
 Fragaria vesca plants germinated and grown in controlled conditions. To
 assess the stability of spatial epigenetic variation in the presence of an
 environmental stressor, we applied acute drought stress to part of the
 plants and quantified drought-induced changes in DNA methylation
 signatures. We find that epigenetic memories and genomic islands of
 epigenetic divergence arise even at fine spatial scale, and that distinct
 spatial scales are featured by distinct epigenetic patterns. For example,
 demethylation of transposable elements consistently occurred at the large
 but not the fine spatial scale, while methylation differentiation for most
 biological processes were shared between spatial scales. Acute drought
 stress did not result in significant epigenetic differentiation. Our
 results indicate that population history, rather than short-term
 environmental stress, plays a dominant role in shaping epigenetic
 signatures. Specifically, repeated historical stress levels associated
 with heterogeneous environmental conditions may be required for acquiring
 a stable epigenetic memory and for coping with future environmental
 change.
description: Whole genome bisulfite sequencing was used to identify methylated
 cytosines across 30 genomes of wild woodland strawberries raised in a
 common garden. The seeds were collected in France (west and east) and
 Poland (west). Differentially methylated cytosines (DMCs) were called
 using the<i> </i>R package methylKit version 1.10.0 with
 conventional DMC parameters (Akalin <i>et al.</i> 2012).
 Specifically, only cytosines with at least 5x coverage in at least 3
 samples per group were retained (Walker <i>et al.</i> 2015;
 Wan <i>et al.</i> 2016). To reduce bias due to outlier depth,
 bases with a read depth above the 99.9th percentile of coverage are
 filtered out. The filtered data were used to test for differentially
 methylated cytosines (DMCs), considering a 25% difference and q-values
 &lt;0.01 as significant. DMCs were identified between (i) low, mid and
 high altitudinal samples (hereafter “altitudinal DMCs”), (ii) three
 distance European samples (hereafter “spatial DMCs”), and (iii) two soil
 moisture treatments (hereafter “drought DMCs”).
description: The dataset includes statistically
 significant DMCs (differentially methylated cytosines) along a fine-scale
 altitudinal gradient, a large-scale spatial gradient, and between soil
 moisture treatments, along with methylation proportions at each sampled
 location, and whether or not the genes alining with the
 F.
 vesca genome were involved with
 transposon
 activity.