DOI: 10.5061/dryad.1b01r
title: Data from: Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients

description: DNA methylation in plants affects transposon silencing, transcriptional
 regulation and thus phenotypic variation. One unanswered question is
 whether DNA methylation could be involved in local adaptation of plant
 populations to their environments. If methylation alters phenotypes to
 improve plant response to the environment, then methylation sites or the
 genes that affect them could be a target of natural selection. Using
 reduced-representation bisulphite sequencing (RRBS) data, we assessed
 whether climate is associated with variation in DNA methylation levels
 among 58 naturally occurring, and species-wide samples of valley oak
 (Quercus lobata) collected across climate gradients. We identified the
 genomic context of these variants referencing a new draft valley oak
 genome sequence. Methylation data were obtained for 341 107 cytosines, of
 which we deemed 57 488 as single-methylation variants (SMVs), found in the
 CG, CHG and CHH sequence contexts. Environmental association analyses
 revealed 43 specific SMVs that are significantly associated with any of
 four climate variables, the majority of which are associated with mean
 maximum temperature. The 43 climate-associated SMVs tend to occur in or
 near genes, several of which have known involvement in plant response to
 environment. Multivariate analyses show that climate and spatial variables
 explain more overall variance in CG-SMVs among individuals than in SNPs,
 CHG-SMVs or CHH-SMVs. Together, these results from natural oak populations
 provide initial evidence for a role of CG methylation in locally adaptive
 evolution or plasticity in plant response.
description: Methylation
 dataTab-separated file
 containing all 1.47 M methylation level calls (rows) for CG, CHG, or CHH
 sequence contexts (Column 4) across all 58 samples (Columns 5-62)
 investigated in this study. Columns 1-5 give sequence context relative to
 reference genome sequence. Methylation call data were generated from
 BS-Seeker2 and have minimum coverage of 10×.set3.meth.full.tab.gzRedundancy analysis input and output filesRedundancy analysis (RDA) was performed in VEGAN 2.3 in R 3.1.2 with SMVs (or SNPs) as dependent variables and climate and spatial variables as independent variables, separately for each SMV context and for SNPs. Permutation tests ('anova' function) with 999 permutations were used to assess the significance of the associations. Spatial variables included longitude ("Lon" in CLIMforRDA.txt) and latitude ("Lat") as Albers x/y coordinates, as well as elevation.RDAfiles.tar.gzPyLMM input and output filesWe used linear mixed models implemented in PYLMM (http://genetics.cs.ucla.edu/pylmm/index.html) to test for specific SMV with significant association with climate variables after correcting for kinship. We used the methylation data to estimate the kinship matrix because we determined that it captures the relatedness of individuals, and better controls the rate of false positives than using the SNP data for estimating kinship.PyLMMfiles.tar.gzSNP dataSNP data in standard VCF format. Target genomic intervals for variant calling were identified using GATK’s CallableLoci. To avoid spurious calls at the edges of the RRBS target regions, the target intervals were trimmed by three bases on each end. Bwa-meth was used to align the reads for input to Bis-SNP. Bis-SNP’s BisulfiteGenotyper was run with the following parameters: -stand_call_conf 4 -stand_emit_conf 0 –maximum_read_cov 100000 –mm40 10 –trim5 2 –trim3 2 –mmq 10 –mbq 15 –useBAQ. GATK’s VariantFiltration and SelectVariants were used to remove calls for sites with low depth of coverage (DP &lt; 4), restrict to diallelic sites, and filter variants based on the following GATK variant annotation cutoffs, QD &lt; 2.0, MQ &lt; 40.0, MQRankSum &lt; −12.5, ReadPosRankSum &lt; −8.0, and AF &lt; 0.1.set3.snps.vcf.gzBAM filesBAM files generated from BS-Seeker2 with bowtie alignerBAMs.zip