Water lilies sit near the base of the flowering-plant tree, making them valuable for studying the earliest steps in angiosperm evolution. Yet their genomes are often difficult to assemble because many species have large, repeat-rich, or polyploid genomes. At the same time, their lives unfold in unstable aquatic habitats where leaves may shift from submerged conditions to drying air, while seeds must germinate quickly in microbe-rich water. Draft genomes can miss repetitive regions that may contain important regulatory information. Based on these challenges, there is a need to conduct in-depth research on complete water lily genomes and the developmental regulatory systems that help ancient aquatic plants adapt to changing environments.
Published (DOI: 10.1093/hr/uhag085) on 4 March 2026 in Horticulture Research, the study was conducted by researchers from Hainan University and Nanjing Agricultural University. The team generated a telomere-to-telomere (T2T), gap-free genome assembly of the miniature water lily Nymphaea minuta using high-fidelity (HiFi) long-read sequencing and high-throughput chromosome conformation capture (Hi-C). They further integrated 165 ribonucleic acid sequencing (RNA-seq) samples from 15 organs and developmental stages to map how this ancient aquatic plant regulates growth, stress response, and seed establishment.
The assembly resolved all 14 chromosomes without gaps, including 27 telomeres and 14 centromeres, and annotated 21,860 protein-coding genes. This makes Nymphaea minuta a cleaner and more compact reference than several related water lilies, strengthening its value as a laboratory model. The transcriptome atlas grouped samples into seven developmental trajectories: architecture, blade, flower, fruit, underground organs, seed, and seedling. It also identified 1,179 organ-specific genes, including stamen-associated genes linked to floral scent chemistry and leaf-associated genes tied to meristem maintenance and delayed senescence. Under water-loss stress, the study uncovered a two-step leaf response. First, a surface-sensing module and mitogen-activated protein kinase (MAPK) signaling help trigger rapid protective responses. As drought becomes severe, the plant shifts to post-transcriptional remodeling: the LSM1B, LSM2, and ENOCgenes activate RNA degradation machinery that may clear nonessential messenger RNAs (mRNAs), conserving energy until water returns. During germination, the MLS gene supports the glyoxylate cycle, while ERF1-family transcription factors encoded by Nmin_6G000717 and Nmin_12G001018connect ethylene, abscisic acid (ABA), and jasmonic acid (JA) signaling with defense-related PR1genes. Together, these modules describe a plant that does not simply endure environmental stress, but actively switches between growth, survival, and recovery programs.
The authors said the study shows how a small water lily can carry a large evolutionary message. They said the complete genome is not only a reference sequence, but a living map of how ancient flowering plants manage risk: leaves use an early-warning system for drying, while seeds turn stored energy into growth without leaving young seedlings defenseless. This combined view of genome structure and gene activity, they said, helps explain how water lilies remain both ancient in origin and highly flexible in modern environments.
Application and implications: Beyond evolutionary biology, the work provides practical tools for aquatic plant research, breeding, and conservation. A gap-free reference genome can help researchers locate genes linked to ornamental traits such as flower form, scent, color, and growth habit, while the stress-response models point to candidate pathways for improving resilience in aquatic crops and garden water lilies. Nymphaea minuta is small, diploid, easy to cultivate, produces many seeds, and can also be maintained through tubers, making it suitable for repeatable laboratory studies. As climate change increases the frequency of water fluctuation, this miniature water lily may become a powerful model for understanding how plants survive at the edge between water and land.
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References
DOI
10.1093/hr/uhag085
Original Source URL
https://doi.org/10.1093/hr/uhag085
Funding information
F.C. was supported by the National Natural Science Foundation of China (32172614) and a grant from Hainan University (XTCX2022NYB04)
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.