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

Gugger PF, Fitz-Gibbon S, Pellegrini M, Sork VL

Date Published: February 4, 2016

DOI: http://dx.doi.org/10.5061/dryad.1b01r

 

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Title Methylation data
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Description 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×.
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Title Redundancy analysis input and output files
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Description 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.
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Title PyLMM input and output files
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Description 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.
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Title SNP data
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Description 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.
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Title BAM files
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Description BAM files generated from BS-Seeker2 with bowtie aligner
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When using this data, please cite the original publication:

Gugger PF, Fitz-Gibbon S, Pellegrini M, Sork VL (2016) Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients. Molecular Ecology 25(8): 1665-1680. http://dx.doi.org/10.1111/mec.13563

Additionally, please cite the Dryad data package:

Gugger PF, Fitz-Gibbon S, Pellegrini M, Sork VL (2016) Data from: Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1b01r
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