The evolutionary history of the ANA-grade angiosperms provides a crucial window into the transition of early flowering plants. Within this group, the Nymphaeales (water lilies) are pivotal, yet a lack of gapless genomic resources has hindered research into their complex developmental and adaptive programs. In this study, we present a telomere-to-telomere (T2T), gap-free genome assembly of Nymphaea minuta, a miniature water lily endemic to Madagascar. Utilizing PacBio Revio HiFi and Hi-C technologies, we generated a 382-Mb assembly anchored to 14 chromosomes. Comparative analysis reveals a compact genome with lower levels of ancient polyploidization than other Nymphaeaceae. By integrating a comprehensive transcriptome atlas of 15 organs and developmental stages, we identified seven primary developmental trajectories and 1179 organ-specific genes. Our analysis uncovered two critical regulatory models: Sequential Dual-Module Relay: In leaves, water fluctuation triggers an initial MAPK-signaling stress response, followed by a post-transcriptional ‘transcriptome reset’ mediated by the RNA degradation pathway (LSM1/2 and ENOC) during severe drought. Energy-Program Coordination: Seed development is governed by a three-phase transition where the glyoxylate cycle (MLS) drives energy mobilization, while an ERF1-centered hub integrates ethylene, ABA, and JA signaling to balance rapid germination with immune defense. These findings provide a definitive genomic reference for basal angiosperms and elucidate the molecular networks enabling the survival and rapid development of these ancient aquatic herbs.

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