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

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 GuZhong Hua Chen, Klaus F.X. Mayer, Xiaofan Zhou, Jihua Wang, Liangsheng Zhang

School of Science

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

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.

Original language	English
Article number	45
Journal	Nature Communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-024-55545-8
Publication status	Published - Dec 2025

Bibliographical note

Publisher Copyright:
© The Author(s) 2024.

Access to Document

10.1038/s41467-024-55545-8

Cite this

Liang, Y., Gao, Q., Li, F., Du, Y., Wu, J., Pan, W., Wang, S., Zhang, X., Zhang, M., Song, X., Zhong, L., Zhang, F., Li, Y., Wang, Z., Li, D., Duan, Q., Li, S., Jin, C., Zhang, P., ... Zhang, L. (2025). The giant genome of lily provides insights into the hybridization of cultivated lilies. Nature Communications, 16(1), Article 45. https://doi.org/10.1038/s41467-024-55545-8

@article{51582bf3277444ab910631271739e01c,

title = "The giant genome of lily provides insights into the hybridization of cultivated lilies",

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.",

author = "Yuwei Liang and Qiang Gao and Fan Li and Yunpeng Du and Jian Wu and Wenqiang Pan and Shaokun Wang and Xiuhai Zhang and Mingfang Zhang and Xiaoming Song and Linlin Zhong and Fan Zhang and Yan Li and Zhiwei Wang and Danqing Li and Qing Duan and Shenchong Li and Chunlian Jin and Peihua Zhang and Yang Gu and Chen, {Zhong Hua} and Mayer, {Klaus F.X.} and Xiaofan Zhou and Jihua Wang and Liangsheng Zhang",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2025",

month = dec,

doi = "10.1038/s41467-024-55545-8",

language = "English",

volume = "16",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

Liang, Y, Gao, Q, Li, F, Du, Y, Wu, J, Pan, W, Wang, S, Zhang, X, Zhang, M, Song, X, Zhong, L, Zhang, F, Li, Y, Wang, Z, Li, D, Duan, Q, Li, S, Jin, C, Zhang, P, Gu, Y, Chen, ZH, Mayer, KFX, Zhou, X, Wang, J & Zhang, L 2025, 'The giant genome of lily provides insights into the hybridization of cultivated lilies', Nature Communications, vol. 16, no. 1, 45. https://doi.org/10.1038/s41467-024-55545-8

TY - JOUR

T1 - The giant genome of lily provides insights into the hybridization of cultivated lilies

AU - Liang, Yuwei

AU - Gao, Qiang

AU - Li, Fan

AU - Du, Yunpeng

AU - Wu, Jian

AU - Pan, Wenqiang

AU - Wang, Shaokun

AU - Zhang, Xiuhai

AU - Zhang, Mingfang

AU - Song, Xiaoming

AU - Zhong, Linlin

AU - Zhang, Fan

AU - Li, Yan

AU - Wang, Zhiwei

AU - Li, Danqing

AU - Duan, Qing

AU - Li, Shenchong

AU - Jin, Chunlian

AU - Zhang, Peihua

AU - Gu, Yang

AU - Chen, Zhong Hua

AU - Mayer, Klaus F.X.

AU - Zhou, Xiaofan

AU - Wang, Jihua

AU - Zhang, Liangsheng

PY - 2025/12

Y1 - 2025/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85213976922&partnerID=8YFLogxK

U2 - 10.1038/s41467-024-55545-8

DO - 10.1038/s41467-024-55545-8

M3 - Article

AN - SCOPUS:85213976922

SN - 2041-1723

VL - 16

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 45

ER -

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

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this