Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense

This repository stores data produced from a genomic and epigenomic large-scale survey of natural populations of Thlaspi arvense, investigating the genetic and environmental bases of epigenetic variation. 207 lines from across Europe were grown in common environment and scored for genetic and DNA methylation variation by Whole Genome Sequencing and Whole Genome Bisulfite Sequencing respectively. This repository includes:

1) The original mean methylation values for all lines, the respective processed values (corrected for non-conversion rate by subtracting the "Surplus_0.6NCR", and optionally corrected for coverage and transformed), used for Genome Wide Association Studies (GWAS) and correlation with climatic variables. In addition, the weighted methylation values (Schultz et al. 2012) are available.

2) Differentially Methylated Regions and Variance Decomposition Analysis results, obtained with scripts available at https://github.com/Dario-Galanti/popDMRs_refine_VCA.

3) Gene Body Methylation (GBM) classification for each line and sequence context. A binomial test was applied to each coding sequence (CDS) to determine if its fraction of methylated cytosines was higher than average (Takuno and Gaut 2013). A 0 indicates a non-significant test, a 1 indicates a significant test. Code available at https://github.com/Dario-Galanti/WGBS_downstream/tree/main/WGBS_completeworkflow.

4) GWAS results (filtered for -log(p)>1) for all processed mean methylation values are available with the ".gwas" extention and can be opened with Integrative Genomics Viewer (https://software.broadinstitute.org/software/igv/), using the reference genome published by Nunn et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34990041/).