Seagrasses are clonal plants playing fundamental roles in coastal ecosystems, yet their survival is increasingly threatened by climate‑driven stressors, namely marine heatwaves. To cope with recurring stress, they rely on stress memory mechanisms associated with priming, whereby prior exposure to a stressor enhances future tolerance. In terrestrial species, this process is mediated by epigenetic regulation, particularly DNA methylation, which modulates gene expression. However, the molecular basis of stress memory in seagrasses, and its persistence across clonal generations, remain unexplored. This study addressed this knowledge gap by building on a previous thermal priming experiment in Cymodocea nodosa, analyzing the expression of candidate genes selected according to differential methylation patterns across thermal treatments and clonal generations. Results indicate that global gene expression variation is driven by clonal generation and stress exposure, while priming-related responses were limited to specific genes. Moreover, only a weak association between DNA methylation and gene expression was observed, with no consistent relationships detected for individual genes. Overall, these findings suggest that heat stress memory and its inheritance in C. nodosa are governed by complex, gene-specific interactions between DNA methylation and gene expression across clonal generations, and that the relation between methylation and gene expression is not always linear.
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