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Water lily complete genomes illuminate the innovations of water lilies and early angiosperms

Nature Plants (2026) Cite this article

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Abstract

Water lilies are among the most basal groups of angiosperms and retain many morphological and physiological traits of early angiosperms, making them invaluable for studying angiosperm evolution, particularly floral organ development. Here we present the most comprehensive phylogeny of the genus Nymphaea to date, alongside gap-free genome assemblies for three species (Nymphaea colorata, Nymphaea thermarum and Nymphaea caerulea). Our analyses resolve 2 major clades, day-flowering (section A) and night-flowering (section B), which diverged approximately 50 million years ago. Comparative genomics reveals an angiosperm-exclusive pectin lyase gene specifically expressed during pollen tube elongation. Regarding floral traits, we identify the transcription factor NcolMYB75-like as a master regulator of blue anthocyanin biosynthesis. Furthermore, the expansion and diversification of the O-methyltransferase gene family drive the synthesis of species-specific floral scent volatiles. These findings deepen our understanding of early angiosperm innovations and provide a genomic framework for plant breeding and ecological conservation.

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Fig. 1: Phylogeny and biogeography of Nymphaea.
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Fig. 2: Genomic assembly features and synteny analysis.
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Fig. 3: Ancestral karyotype reconstruction and chromosomal evolution of Nymphaeales.
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Fig. 4: Gene family/orthogroup gains during the evolution of angiosperms identify the novel pectin lyase that enables pollination.
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Fig. 5: Loss of genes in the water lilies reveal the genes that may be responsible for aquatic life of water lilies.
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Fig. 6: Metabolic profiling and genetic analysis of N. colorata cultivars with distinct floral pigmentation.
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Fig. 7: The floral scent compounds and OMT phylogenic tree in Nymphaea species.
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Data availability

All raw sequencing data have been deposited in the National Genomics Data Center. Data used for genome assembly and gene expression quantification are available under project accession numbers PRJCA040347 (N. caerulea), PRJCA021382 (N. thermarum), PRJCA027228 (N. colorata) and PRJCA033981 (Nymphaea sp. Peru–Puerto Maldonado). Data used for flower colour-regulatory analysis are available under project accession number PRJCA023065. Transcriptomic data used for phylogenetic reconstruction of Nymphaea are available under project accession number PRJCA030030. Source data are provided with this paper.

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Acknowledgements

F.C. was supported by the National Natural Science Foundation of China (32172614) and a grant from Hainan University (XTCX2022NYB04). J.-Y.X. acknowledges funding from the National Natural Science Foundation of China (32570265), the Basic Research Program of Jiangsu (BK20252062), the Fundamental Research Funds for the Central Universities (RENCAI2025034 and KYCXJC2025002), the National Administration of Traditional Chinese Medicine High-level Key Discipline Construction Project (zyyzdxk-2023293) and the Traditional Chinese Medicine Interdisciplinary Cultivation Project. We thank J. Qiu for the myb75-c mutant seeds.

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Author notes

  1. These authors contributed equally: Ji Zhang, Yufan Liang, Guanhua Liu, Yang Bai, Xin-Cheng Huang.

Authors and Affiliations

  1. Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China

    Ji Zhang, Yufan Liang, Hongbin Zhang, Hongliang Chen, Wenquan Wang & Fei Chen

  2. College of Tropical Agriculture and Forestry, Hainan University, Danzhou, China

    Ji Zhang, Yufan Liang, Hongbin Zhang, Hongliang Chen, Wenquan Wang & Fei Chen

  3. Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China

    Guanhua Liu & Jianyu Fu

  4. Jiangsu Key Laboratory for Conservation and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China

    Yang Bai

  5. College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China

    Xin-Cheng Huang, Yifan Jiang & Jia-Yu Xue

  6. National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China

    Yibo Bai

  7. Agronomy Department of Superior School Engineering, University of Almería, Almeria, Spain

    Pedro Garcia-Caparros

  8. Hainan Fodu Lianyuan Ecological Agriculture Co. Ltd, Haikou, China

    Tianlong Zhu

  9. Agriculture and Biotechnology, Zhejiang University, Hangzhou, China

    Liangsheng Zhang

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Contributions

F.C. conceived this study. J.-Y.X. and Y.J. participated in and coordinated the research. J.Z., Y.L., G.L, Yang Bai, X.-C.H., Yibo Bai, P.G.-C., T.Z., J.F., H.Z., H.C., W.W. and L.Z. conducted the genomic analyses and laboratory experiments. J.Z., Y.L., F.C., J.-Y.X. and Y.J. drafted the paper. F.C. and J.-Y.X. edited the paper. The authors read and approved the final paper.

Corresponding authors

Correspondence to Yifan Jiang, Jia-Yu Xue or Fei Chen.

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Patent applications related to this work have been submitted by J.Z., Yang Bai and F.C. The other authors declare no competing interests.

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Nature Plants thanks Yuannian Jiao and Jianquan Liu for their contribution to the peer review of this work.

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Source data

Source Data Fig. 1 (download XLSX )

Data for tree construction.

Source Data Fig. 2 (download XLSX )

Whole genomic details for circos plots.

Source Data Fig. 4 (download XLSX )

Data of gene family expansion and contraction.

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List of lost genes and their GO annotation.

Source Data Fig. 6 (download XLSX )

Details for coexpression gene network and anthocyanin quantification data.

Source Data Fig. 7 (download XLSX )

Expression pattern of OMTs from three water lilies.

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Zhang, J., Liang, Y., Liu, G. et al. Water lily complete genomes illuminate the innovations of water lilies and early angiosperms. Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02281-0

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