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.