Liang Yuwei, Gao Qiang, Li Fan, Du Yunpeng, Wu Jian, Pan Wenqiang, Wang Shaokun, Zhang Xiuhai, Zhang Mingfang, Song Xiaoming, Zhong Linlin, Zhang Fan, Li Yan, Wang Zhiwei, Li Danqing, Duan Qing, Li Shenchong, Jin Chunlian, Zhang Peihua, Gu Yang, Chen Zhong-Hua, Mayer Klaus F X, Zhou Xiaofan, Wang Jihua, Zhang Liangsheng
Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Hangzhou, China.
Yunnan Seed Laboratory, Kunming, China.
Nat Commun. 2025 Jan 2;16(1):45. doi: 10.1038/s41467-024-55545-8.
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.
百合是重要的单子叶植物，以其观赏花卉、鳞茎和庞大的基因组而闻名。其基因组信息的缺失阻碍了进化研究和基于基因组的育种工作。在此，我们展示了岷江百合（百合，35.66 Gb）和火焰百合（5.09 Gb）的参考基因组。巨型百合基因组由近期的长末端重复逆转座子塑造。系统发育分析揭示了百合栽培品种多样的、独立的起源。参与蔗糖和淀粉代谢的基因家族在百合基因组中显著扩增。XTH22、SOC1和AP1/FUL样基因的关键同源物调控百合鳞茎的发育、芽生长转变和花芽生长转变。在火焰百合中鉴定出秋水仙碱生物合成基因簇，但在岷江百合中不存在，这突出了秋水仙科中秋水仙碱的独立进化。这些基因组见解增强了对百合目进化的理解，为未来的育种和分子研究奠定了基础。
