Sun Meiyu, Han Baocai, Xiao Jianhua, Yu Haiyan, Jia Yinli, Yuan Shuhai, Yao Juan, Xing Quan, Wu Dongqi, Sun Guofeng, Zhang Jinzheng
China National Botanical Garden, Beijing, 100093, China.
State Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Institute of Botany, Beijing, 100093, China.
BMC Plant Biol. 2025 Jul 4;25(1):874. doi: 10.1186/s12870-025-06863-6.
Hemerocallis middendorffii is a kind of high quality ornamental plant with strong cold resistance, pleasant aroma, and gorgeous floral color. Hemerocallis is one of the three internationally recognized perennial flowers that has huge demand in the flower market. However, little is known about the floral scent and color biosynthesis in daylily due to the large genome size. RESULTS: We reported here a high-quality chromosome-scale genome of H. middendorffii which was a native daylily in China. Using PacBio HiFi and Hi-C sequencing technologies, we assembled a chromosome-level genome of 4.10 Gb with a contig N50 of 12.81 Mb. We identified 65,536 protein-coding genes across the 11 chromosomes. We employed a combination of genomic, transcriptomic, and metabolomic approaches to investigate mechanisms behind the floral scent and color biosynthesis in daylily. The main terpenoids contributing to floral fragrance were linalool, 3-carene, nerolidol, and α-farnesene, while carotenoids and anthocyanidins were the main components of floral color. These traits could be stably inherited by their hybrid progenies, and some of them exhibited heterosis. Through Weighted Gene Co-expression Network Analysis (WGCNA) analysis, we identified two modules MEblueviolet and MEgreenyellow related to terpenoids (floral scents) and carotenoids (floral colors) biosynthesis. The 10 hub genes including DXS, MVD, MVK, DXR, LCYBs, Z-ISO, CYPs, and JAS were screened by network construction. The results of qRT-PCR analysis showed that these hub genes were significant differentially expressed in daylily samples, and these results were basically consistent with the relative transcript levels of RNA-seq. CONCLUSIONS: This study not only provides new insights into the molecular mechanisms of floral scent and color, but also lays a foundation for subsequent research on key gene functions and molecular breeding in Hemerocallis.
黄花菜是一种优质的观赏植物，具有很强的抗寒性，香气宜人，花色艳丽。萱草是国际公认的三大宿根花卉之一，在花卉市场上需求量巨大。然而，由于基因组规模较大，关于黄花菜花香和花色生物合成的研究较少。结果：我们在此报告了中国本土黄花菜——北黄花菜的高质量染色体级基因组。利用PacBio HiFi和Hi-C测序技术，我们组装了一个大小为4.10 Gb的染色体级基因组，重叠群N50为12.81 Mb。我们在11条染色体上鉴定出65536个蛋白质编码基因。我们采用基因组、转录组和代谢组学相结合的方法，研究黄花菜花香和花色生物合成的机制。对花香有贡献的主要萜类化合物有芳樟醇、3-蒈烯、橙花叔醇和α-法呢烯，而类胡萝卜素和花青素是花色的主要成分。这些性状可以由它们的杂交后代稳定遗传，其中一些表现出杂种优势。通过加权基因共表达网络分析（WGCNA），我们鉴定出了与萜类化合物（花香）和类胡萝卜素（花色）生物合成相关的两个模块MEblueviolet和MEgreenyellow。通过网络构建筛选出了包括DXS、MVD、MVK、DXR、LCYBs、Z-ISO、CYPs和JAS在内的10个核心基因。qRT-PCR分析结果表明，这些核心基因在黄花菜样本中显著差异表达，这些结果与RNA-seq的相对转录水平基本一致。结论：本研究不仅为花香和花色的分子机制提供了新的见解，也为黄花菜后续关键基因功能研究和分子育种奠定了基础。
