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

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, Qing Duan, Shenchong Li, Chunlian Jin, Peihua Zhang, Yang Gu, Zhong-Hua Chen, Klaus F. X. Mayer (), Xiaofan Zhou (), Jihua Wang () and Liangsheng Zhang ()
Additional contact information
Yuwei Liang: Zhejiang University
Qiang Gao: Zhejiang University
Fan Li: Yunnan Seed Laboratory
Yunpeng Du: Beijing Academy of Agriculture and Forestry Sciences
Jian Wu: Agricultural University
Wenqiang Pan: Beijing Academy of Agriculture and Forestry Sciences
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
Shenchong Li: Yunnan Seed Laboratory
Chunlian Jin: Yunnan Seed Laboratory
Peihua Zhang: Yunnan Seed Laboratory
Yang Gu: Yunnan Agricultural University
Zhong-Hua Chen: Western Sydney University
Klaus F. X. Mayer: Helmholtz Center Munich
Xiaofan Zhou: South China Agricultural University
Jihua Wang: Yunnan Seed Laboratory
Liangsheng Zhang: Zhejiang University

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-024-55545-8

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