Data from: Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing

Epigenetic mechanisms represent a possible mechanism for achieving a rapid response of long‐lived trees to changing environmental conditions. However, our knowledge on plant epigenetics is largely limited to a few model species. With increasing availability of genomic resources for many tree species, it is now possible to adopt approaches from model species that permit to obtain single‐base pair resolution data on methylation at a reasonable cost. Here, we used targeted bisulfite sequencing (TBS) to study methylation patterns in the conifer species Norway spruce (Picea abies). To circumvent the challenge of disentangling epigenetic and genetic differences, we focused on four clone pairs, where clone members were growing in different climatic conditions for 24 years. We targeted >26.000 genes using TBS and determined the performance and reproducibility of this approach. We characterized gene body methylation and compared methylation patterns between environments. We found highly comparable capture efficiency and coverage across libraries. Methylation levels were relatively constant across gene bodies, with 21.3 ± 0.3%, 11.0 ± 0.4% and 1.3 ± 0.2% in the CG, CHG, and CHH context, respectively. The variance in methylation profiles did not reveal consistent changes between environments, yet we could identify 334 differentially methylated positions (DMPs) between environments. This supports that changes in methylation patterns are a possible pathway for a plant to respond to environmental change. After this successful application of TBS in Norway spruce, we are confident that this approach can contribute to broaden our knowledge of methylation patterns in natural tree populations.Pabies1.0-HC.1000mRNA1000Reference fasta file used for mapping the reads containing all high confidence genes from the Picea genome (Nystedt et al. 2013) with 1000 bp before and after the mRNA if availablePabies1.0-HC.1000mRNA1000.gene.sortedgff file with annotations for CDS regions of the high confidence genes in the Picea abies genome (Nystedt et al. 2013)Pabies1.0-HC.1000mRNA1000.probes.sortedgff file with information on all probe regions in the SeqCap Epi probe set used in this publicationmethylation_bed_filesbed files with information on methylation status for CG, CHG and CHH methylation in the eight sequenced libraries