Integrated transcriptomic and metabolomic analyses reveal biphasic thermal adaptation strategies in <i>Lavandula angustifolia</i> under high-temperature stress

Background Lavandula angustifolia is a commercially vital medicinal plant, but its molecular adaptation mechanisms under high-temperature stress (HTS) remain poorly understood. Global warming poses a significant threat to agricultural productivity, necessitating deeper insights into plant thermotolerance strategies for develop climate-resilient crops. Methods We employed integrated transcriptomic and metabolomic analyses to investigate the biphasic responses of L. angustifolia to HTS. Seedlings were subjected to short-term (1–5 h) and long-term (3–5 days) heat stress at 38 °C. Physiological parameters, including malondialdehyde (MDA) and proline (PRO) levels, were measured. Transcriptomic sequencing and metabolomic profiling were conducted to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). Functional enrichment and pathway analyses were performed to elucidate key molecular mechanisms. Results Short-term responses featured rapid Ca 2+ -mediated signaling, heat-shock protein activation, and transient oxidative stress, accompanied by osmoprotectant accumulation ( e.g. , proline and raffinose-family oligosaccharides). Long-term adaptation involved systemic metabolic reorganization, including enhanced citrate cycle (TCA cycle) flux, glyoxylate metabolism, and phenylpropanoid biosynthesis. Key regulators such as aconitate hydratase and galactinol synthase, along with signature metabolites like 2-oxoadipic acid and capric acid, were identified as markers of thermal adaptation. The study reveals a transition from immediate protective responses to sustained metabolic optimization, providing a comprehensive framework for understanding L. angustifolia ’s thermotolerance. These findings offer actionable targets for breeding heat-resistant cultivars to mitigate climate change impacts on medicinal crop production.