The ‘Genomes and Bioinformatics’ work package laid the methodological foundation for epigenomic analysis in the EpiDiverse study species. This work package generated an annotated reference genome for Black poplar and contributed to a reference genome for Field pennycress. Novel bioinformatic tools were generated for: (1) inferring genetic information from bisulfite-converted DNA samples (which are typically used for DNA methylation analysis), (2) the annotation of small RNAs and active transposable elements, (3) improving reference genomes by reconciling different assemblies, (4) optimizing DNA methylation analysis when no reference genome is available. Best-practices bioinformatic pipelines were created. These combined existing and novel tools for (1) the DNA methylation analysis using whole-genome bisulfite sequencing data (WGBS pipeline), (2) identifying genomic regions that are differentially methylated between experimental groups (DMR pipeline), and (3) finding associations between DNA methylation, climatic variation, and underlying genetic variation in samples from natural plant populations (EWAS pipeline).
The 'Natural Patterns' work package applied the best-practices pipelines to natural populations of the three focal plant species, and to plant species exposed to specific ecological conditions. Experiments in this work package were based on extensive field sampling throughout Europe, subsequent common garden experiments, and large-scale DNA methylation screening. This work was supplemented in some species with genetic variation analysis and gene expression analysis. Results show in all three focus species that environmental and genetic factors impact different components of DNA methylation in plant genomes. Asexually reproducing species showed a multi-generation epigenetic memory of stress exposure. Furthermore, experimental manipulation of DNA methylation in living plants indicated that DNA methylation plays a functional role in local adaptation and in plant herbivory responses.
The ‘Molecular Mechanisms’ work package characterized in detail the epigenetic response of plants when exposed to different experimental stress conditions. Many stress environments triggered only modest epigenetic responses, but some stresses (specifically drought and heat) triggered very strong responses. Some of these epigenetic changes were clonally propagated for three generations, but the functional consequences of this transgenerational epigenetic memory were relatively weak.
EpiDiverse organized four summer schools as the basis of the ESRs’ training programme, on plant ecological epigenetics; bioinformatic skill development; data analysis for linking epigenetic to environmental and genetic data; and translating and communicating science. The network hosted 37 extended research visits (2-3 per ESR) in which each ESR gained training experience both in academic and non-academic environments. For dissemination of scientific results, in addition to scientific publications and conference presentations by the ESRs, EpiDiverse organized one open scientific conference that highlighted project results for a broader scientific community. A key output of the network’s dissemination and utilization efforts has been the development of an open, online learning portal for plant epigenetics. This portal is meant for end users as a resource for learning and teaching on plant ecological epigenetics. It includes online lectures, unlocks the bioinformatic analysis pipelines, and contains an online text book on plant ecological epigenetics with chapters that are written by the ESRs. Public outreach was achieved via an EpiDiverse YouTube channel (containing for instance 15 short movies in which the ESRs present their own research) and via participation in the European Researchers Night 2020.
