Seasonal fluctuations strongly shape the physiology of long-lived trees by coordinating growth, dormancy, and stress responses. Increasing evidence points to epigenetic mechanisms, particularly DNA methylation, as regulators of these processes, yet their role in long-lived trees across seasons, developmental stages and generations remains poorly understood. We generated single-base resolution maps of cytosine methylation exploring the epigenetic landscape of 180 year-old mature oak (Quercus robur) trees (genetically homogeneous) along spring, summer and autumn, and in their progeny. Genome-wide DNA-methylation revealed a progressive increase in the CHH context (H = A, T or C) from Spring to Summer and Autumn, suggesting epigenetic reprogramming is happening over season and growing cycle. Differentially Methylated Regions (DMRs) were concentrated in promoter regions and terminal inverted repeat (TIR) transposons. Observed differentially methylated transposable elements (TEs) and genes were majorly involved in leaf development and hormonal signalling. By contrast, generational differences (parents versus offspring) were most prominent in CG and CHG contexts and were concentrated in genic regions. Oaks exhibit distinct seasonal and generational DNA methylation signatures, highlighting the plasticity and developmental specificity of epigenetic regulation. These findings provide a genomic foundation for understanding how epigenetic memory contributes to phenology, developmental programming and long-term adaptation in long-lived plants.
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