Epigenomic Landscape of Oak (Quercus robur) across Season and Generation.

Molecular regulatory mechanisms of Populus deltoides under combined high temperature and short-photoperiod stress associated with DNA methylation

The molecular mechanisms underlying DNA methylation-associated environmental adaptation in poplar are preliminarily revealed, providing potential genetic targets for breeding climate-resilient trees.

Contrasting plastic and genetic responses of leaf unfolding and senescence to temperature in Quercus petraea.

CHH methylation is recruited to gene-proximal transposable elements during repeated drought stress

These findings support a model in which repeated drought consistently recruits CHH methylation to reproducible gene-proximal TEs, where it is associated with maintenance of local TE repression despite continued activation of neighboring stress-responsive genes.

Comparative genomics of abiotic stress response in Norway spruce and Scots pine

Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are dominant boreal forest species with globally important contributions to carbon capture and storage and sustain an extensive forestry industry. Both species have adapted to cold and episodic drought, yet each occupies a distinct ecological niche. How conserved their stress responses are, which features are lineage-specific, and how far mechanisms known from herbaceous angiosperms apply, remain open questions of importance in the face of ongoing climate change. We profiled roots and needles of both species under drought and cold, combining differential expression with an orthology-aware comparative co-expression framework that places each gene on a conservation–divergence gradient. Differential expression was largely organ- and stress-specific, yet cross-species overlap at the orthogroup level was extensive and increased with stress intensity. Comparative co-expression recovered a further conserved regulatory backbone that per-timepoint differential expression did not resolve, enriched for abscisic-acid-centred signalling, oxidative and osmotic-stress responses and growth suppression, and containing canonical stress response transcription-factor families including NAC, WRKY and bZIP/ABF. The breadth of co-expression conservation for a gene was coupled to purifying selection on its coding sequence and to network connectivity. Additionally, segmental duplicates shared between the species were enriched among conserved drought circuits, whereas lineage-specific duplicates were enriched among genes lacking conserved co-expression. Regulatory conservation and genome architecture thus describe a single conservation–divergence axis, providing an evolution-anchored criterion that helps separate candidate core regulators (which are conserved, network-central and constrained) from reactive change that differential expression alone cannot resolve. Significance statement Cold and drought are recurring threats to boreal forests, yet how conifers coordinate their responses, and how much of that response is evolutionarily conserved, has been difficult to establish. Comparing Norway spruce and Scots pine, two species separated by a deep evolutionary divergence, we show that the genes whose co-expression is most broadly conserved between the species are also those under the strongest purifying selection on their protein-coding sequences. As these two species diverged so long ago, this conserved regulatory core stands out as an evolutionary signal that simple comparisons of differentially expressed genes fail to capture. The approach provides an evolution-anchored way to distinguish genes central to the stress response from lineage-specific or reactive change.

Distinct seasonal acclimatisation trajectories characterize transplanted and natural meadow seagrass plants

Successful establishment is a critical determinant of seagrass restoration, yet the molecular mechanisms underlying seedling acclimatisation to natural environments remain poorly understood. Here, we combined seasonal physiological observations, transcriptome profiling, and gene co-expression network analysis to investigate the mechanisms underlying the early post-transplantation phase of Posidonia oceanica, a dominant foundation seagrass species, following transplantation. Transplanted seedlings were compared with plants from adjacent natural meadows over the first six months after transplantation using leaf and root samples collected in spring, summer, and autumn. Tissue identity was the primary driver of transcriptomic variation, but transplanted seedlings remained transcriptionally distinct from plants in natural meadows throughout the study, with roots showing greater divergence than leaves, suggesting tissue-specific trajectories of post-transplantation acclimatisation. The early post-transplantation phase was characterised by the activation of genes associated with RNA processing, transcriptional regulation, and abscisic acid signalling. During a summer marine heatwave (28 °C), both plant groups induced conserved heat-response pathways, including heat-shock proteins and protein-folding mechanisms. Furthermore, transplanted seedlings maintained higher expression of genes involved in photosystem II repair and photoprotection and exhibited reduced leaf growth and extensive leaf necrosis, consistent with a greater requirement for photosynthetic maintenace under prolonged thermal stress. Gene co-expression network analysis revealed that regulatory networks governing structural integrity, hormone signalling, and defence were more stable in natural meadow plants, while transplanted seedlings progressively reorganized their gene co-expression patterns to resemble those of natural meadow plants, particularly in leaves. Our findings reveal tissue-specific molecular trajectories of acclimatisation during early seedling establishment and identify candidate molecular indicators of field acclimatisation and thermal stress responses, providing new mechanistic insights relevant to seedling-based seagrass restoration under climate change.

Mesoclimatic origin affects alpine plant germination but not its plasticity

Mountain ecosystems are disproportionately exposed to global warming, which may put alpine plant species in particular at risk. Plant species' migration and persistence depend on successful seed regeneration, with demographic traits such as germination being strongly sensitive to both present and ancestral climate. Germination may, thus, present a major bottleneck to alpine plant species under climate change, or they may cope through phenotypic plasticity. However, little is known about alpine plant germination under warming, its plasticity, and whether any of these are co‐determined by the climatic origin of the seeds. We investigated intraspecific variation in germination proportion and timing of six co‐occurring alpine plant species from different micro‐ and mesoclimatic origins as response to three temperature treatments using growth chambers. Elevation as well as topographic strata were used as proxies for mesoclimate and mean soil temperature, growing‐ as well as freezing‐degree‐days for microclimate. Our results show that species were plastic in germination proportion and timing in response to temperature, with all species germinating in the warmest treatment. Micro‐ and mesoclimatic origin affected germination traits but did not co‐determine species responses to the temperature treatments. We also demonstrated maternal climatic effects, with seeds from warmer microclimates displaying higher phenotypic plasticity. Furthermore, seeds originating from colder mesoclimates, i.e. the upper elevation range, generally germinated less. Our results suggest that global warming will impact alpine plant regeneration from seeds through concurrent effects during germination, climatic origin as well as shifts in germination timing. Importantly, our results indicate that regeneration from seed may contribute to defining the upper elevational limit of alpine plant species through climatic origin and maternal microclimatic effects.