A telomere-to-telomere genome assembly of Nymphaea minuta provides details into the developmental transcriptome atlas and adaptive regulatory mechanisms

Abstract

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.

Acknowledgements

F.C. was supported by the National Natural Science Foundation of China (32172614) and a grant from Hainan University (XTCX2022NYB04).

Author contributions

F.C. designed this study. H.C. and Y.L. performed the plant cultivation, sampling, sequencing, data analysis, and wet lab experiment. F.C. drafted the manuscript. J.-Y.X. participated in manuscript drafting. All authors approved the final manuscript.

Data availability

The raw data for the genome sequencing and transcriptome sequencing could be found in NGDC (https://ngdc.cncb.ac.cn/) with project ID: PRJCA021721. Genomic assembly and annotations could be found at https://bioinformatics.hainanu.edu.cn/worp/community/download.

Conflicts of interest statement

The authors declare no conflicts of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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