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; Liangsheng Zhang

doi:10.1038/s41467-024-55545-8

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

Nat Commun. 2025 Jan 2;16(1):45. doi: 10.1038/s41467-024-55545-8.

Authors

Yuwei Liang^#¹, Qiang Gao^#¹, Fan Li^#^{2

3}, Yunpeng Du^#⁴, Jian Wu^#⁵, Wenqiang Pan^{4

5}, Shaokun Wang⁵, Xiuhai Zhang⁴, Mingfang Zhang⁴, Xiaoming Song⁶, Linlin Zhong⁷, Fan Zhang⁷, Yan Li⁸, Zhiwei Wang⁸, Danqing Li⁹, Qing Duan^{2

3}, Shenchong Li^{2

3}, Chunlian Jin^{2

3}, Peihua Zhang^{2

3}, Yang Gu¹⁰, Zhong-Hua Chen^{11

12}, Klaus F X Mayer^{13

14}, Xiaofan Zhou¹⁵, Jihua Wang^{16

17}, Liangsheng Zhang^{18

19

20}

Affiliations

¹ Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Hangzhou, China.
² Yunnan Seed Laboratory, Kunming, China.
³ Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China.
⁴ Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
⁵ Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, Agricultural University, Beijing, China.
⁶ Center for Genomics and Bio-computing, College of Life Sciences, North China University of Science and Technology, Tangshan, China.
⁷ National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China.
⁸ Qi Biodesign, Beijing, China.
⁹ Department of Landscape Architecture, School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, China.
¹⁰ College of Food Science and Technology, Yunnan Agricultural University, Kunming, China.
¹¹ School of Science, Western Sydney University, Penrith, NSW, Australia.
¹² Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
¹³ Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany. [email protected].
¹⁴ School of Life Sciences, Technical University Munich, Munich, Germany. [email protected].
¹⁵ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China. [email protected].
¹⁶ Yunnan Seed Laboratory, Kunming, China. [email protected].
¹⁷ Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China. [email protected].
¹⁸ Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Hangzhou, China. [email protected].
¹⁹ Yazhouwan National Laboratory, Sanya, China. [email protected].
²⁰ State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China. [email protected].

^# Contributed equally.

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.

MeSH terms

Colchicine
Evolution, Molecular
Flowers / genetics
Flowers / growth & development
Gene Expression Regulation, Plant
Genome, Plant*
Hybridization, Genetic*
Lilium* / genetics
Lilium* / growth & development
Multigene Family
Phylogeny*
Plant Breeding
Plant Proteins / genetics
Plant Proteins / metabolism
Retroelements / genetics
Terminal Repeat Sequences / genetics

Substances

Colchicine
Retroelements
Plant Proteins

Abstract

MeSH terms

Substances

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