Data from: Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients

Gugger, Paul F., University of California Los Angeles

Fitz-Gibbon, Sorel, University of California Los Angeles

Pellegrini, Matteo, University of California Los Angeles

Sork, Victoria L., University of California Los Angeles

Published Feb 04, 2016 on Dryad. https://doi.org/10.5061/dryad.1b01r

Cite this dataset

Gugger, Paul F.; Fitz-Gibbon, Sorel; Pellegrini, Matteo; Sork, Victoria L. (2016). Data from: Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients [Dataset]. Dryad. https://doi.org/10.5061/dryad.1b01r

Abstract

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.

Usage notes

Methylation data

Tab-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.gz

Redundancy analysis input and output files

Redundancy 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.gz

PyLMM input and output files

We 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.gz

SNP data

SNP 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 < 4), restrict to diallelic sites, and filter variants based on the following GATK variant annotation cutoffs, QD < 2.0, MQ < 40.0, MQRankSum < −12.5, ReadPosRankSum < −8.0, and AF < 0.1.

set3.snps.vcf.gz

BAM files

BAM files generated from BS-Seeker2 with bowtie aligner

BAMs.zip

Location

United States of America

California