Marine heatwaves (MHWs) are intense climatic events that pose significant threats, extending their effects beyond individual events and affect their response to future extremes. Despite research on MHWs’ effects, their interaction with other global change stressors remains understudied. Although studies have observed physiological and community structure changes caused by MHWs, the underlying molecular mechanisms essential for ecosystem adaptation and response under global change are poorly understood. Here, we investigated changes in physiological performance, DNA methylation, gene and transposable element (TE) expression, across different phases of MHWs and post-MHWs ‘Warming and high CO₂’ conditions in the model diatom Phaeodactylum tricornutum. Our findings revealed that MHWs exposure compromises the P. tricornutum’s capacity to cope with subsequent stress. Gene expression alterations associated with photosynthesis and DNA damage repair pathways, which persist from during MHWs to recovery phase after MHWs, may underlie the reduced resilience to subsequent stress. We found that the expression patterns of TEs across MHWs phases are influenced by their sequence length and GC content. Furthermore, we observed a gradual increase in 5mC methylation in CHG and CHH contexts across different phases, suggesting their important role in response to MHWs. Notably, substantial decrease in adenine methylation (6mA) methylation accompanied by genomic deletions and increased TE expression were observed in the post-MHWs ‘Warming and high CO₂’ phase, highlighting the potential regulatory role of 6mA methylation in modulating TE activity. Our findings underscore the importance of genetic and epigenetic regulation in marine organisms’ acclimation to MHWs.
 

diatoms, DNA methylation, marine heatwaves, ocean acidification, ocean warming, transposons, acclimation