Deciphering genomic adaptations and climate resilience in the intertidal seagrass Zostera japonica

Seagrasses are coastal foundation species that support ecosystem stability but face increasing global change. Here, we assemble a chromosome-level reference genome for the intertidal seagrass Zostera japonica to investigate adaptive evolution and climate resilience. Comparative genomic analyses reveal features underlying intertidal adaptation, including ion transport, circadian regulation, and stress responses. We identify positively selected genes associated with the transition to marine environments. Population genomic analyses identify strong divergence between northern and southern populations, reflecting deep historical separation, largely independent evolutionary trajectories, and local adaptation. Selection signals are enriched in stress response and ion transport genes, among which TIP3-1 confers tolerance to both salinity and heat. Genomic offset projections indicate greater climate vulnerability in northern populations, whereas southern populations show higher adaptive potential and may serve as genetic sources for assisted gene flow. Together, our study provides a genomic framework for understanding adaptation and guiding conservation under climate change.