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The giant genome of lily provides insights into the hybridization of cultivated lilies

Author

Listed:
  • Yuwei Liang

    (Zhejiang University)

  • Qiang Gao

    (Zhejiang University)

  • Fan Li

    (Yunnan Seed Laboratory
    Key Laboratory for Flower Breeding of Yunnan Province)

  • Yunpeng Du

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Jian Wu

    (Agricultural University)

  • Wenqiang Pan

    (Beijing Academy of Agriculture and Forestry Sciences
    Agricultural University)

  • Shaokun Wang

    (Agricultural University)

  • Xiuhai Zhang

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Mingfang Zhang

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Xiaoming Song

    (North China University of Science and Technology)

  • Linlin Zhong

    (Huazhong Agricultural University)

  • Fan Zhang

    (Huazhong Agricultural University)

  • Yan Li

    (Qi Biodesign)

  • Zhiwei Wang

    (Qi Biodesign)

  • Danqing Li

    (Zhejiang Sci-Tech University)

  • Qing Duan

    (Yunnan Seed Laboratory
    Key Laboratory for Flower Breeding of Yunnan Province)

  • Shenchong Li

    (Yunnan Seed Laboratory
    Key Laboratory for Flower Breeding of Yunnan Province)

  • Chunlian Jin

    (Yunnan Seed Laboratory
    Key Laboratory for Flower Breeding of Yunnan Province)

  • Peihua Zhang

    (Yunnan Seed Laboratory
    Key Laboratory for Flower Breeding of Yunnan Province)

  • Yang Gu

    (Yunnan Agricultural University)

  • Zhong-Hua Chen

    (Western Sydney University
    Western Sydney University)

  • Klaus F. X. Mayer

    (Helmholtz Center Munich
    Technical University Munich)

  • Xiaofan Zhou

    (South China Agricultural University)

  • Jihua Wang

    (Yunnan Seed Laboratory
    Key Laboratory for Flower Breeding of Yunnan Province)

  • Liangsheng Zhang

    (Zhejiang University
    Yazhouwan National Laboratory
    Zhejiang A&F University)

Abstract

Lilies are economically important monocots known for their ornamental flowers, bulbs, and large genomes. The absence of their genomic information has impeded evolutionary studies and genome-based breeding efforts. Here, we present reference genomes for Lilium sargentiae (lily, 35.66 Gb) and Gloriosa superba (flame lily, 5.09 Gb). The giant lily genome is shaped by recent long terminal repeat retroelements. Phylogenetic analysis reveals diverse, independent origins of lily cultivars. Gene families involved in sucrose and starch metabolism are significantly expanded in the lily genome. Key homologs of XTH22, SOC1, and AP1/FUL-like genes regulate the development, bud growth transition, and floral bud growth transition of lily bulbs. Colchicine biosynthetic gene clusters are identified in G. superba but are absent in L. sargentiae, highlighting independent colchicine evolution in Colchicaceae. These genomic insights enhance understanding of Liliales evolution, providing a foundation for future breeding and molecular research.

Suggested Citation

  • Yuwei Liang & Qiang Gao & Fan Li & Yunpeng Du & Jian Wu & Wenqiang Pan & Shaokun Wang & Xiuhai Zhang & Mingfang Zhang & Xiaoming Song & Linlin Zhong & Fan Zhang & Yan Li & Zhiwei Wang & Danqing Li & Q, 2025. "The giant genome of lily provides insights into the hybridization of cultivated lilies," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-024-55545-8
    DOI: 10.1038/s41467-024-55545-8
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    References listed on IDEAS

    as
    1. Ryan S. Nett & Warren Lau & Elizabeth S. Sattely, 2020. "Discovery and engineering of colchicine alkaloid biosynthesis," Nature, Nature, vol. 584(7819), pages 148-153, August.
    2. Heqiang Lou & Lili Song & Xiaolong Li & Hailing Zi & Weijie Chen & Yadi Gao & Shan Zheng & Zhangjun Fei & Xuepeng Sun & Jiasheng Wu, 2023. "The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Murukarthick Jayakodi & Agnieszka A. Golicz & Jonathan Kreplak & Lavinia I. Fechete & Deepti Angra & Petr Bednář & Elesandro Bornhofen & Hailin Zhang & Raphaël Boussageon & Sukhjiwan Kaur & Kwok Cheun, 2023. "The giant diploid faba genome unlocks variation in a global protein crop," Nature, Nature, vol. 615(7953), pages 652-659, March.
    4. Ryan S. Nett & Warren Lau & Elizabeth S. Sattely, 2020. "Publisher Correction: Discovery and engineering of colchicine alkaloid biosynthesis," Nature, Nature, vol. 584(7821), pages 35-35, August.
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