植物的生命周期中，从深度休眠到种子萌发的转变是至关重要的，但是中药材紫杉（Taxus chinensis var mairei）中的这一过程如何发生仍不清楚，该中药材是抗癌药物紫杉醇的天然来源。在本文中，我们对中药材紫杉进行了转录组、蛋白质组、空间代谢组和空间脂质组的分析，并展示了紫杉休眠种子和萌发种子的多组学特征。我们的研究结果表明，脱落酸和赤霉素12的稳态与基因转录和蛋白质翻译密切相关，这些植物激素之间的平衡决定了种子是否保持休眠或者萌发。我们发现，在种子萌发过程中，碳水化合物从糖酵解和三羧酸循环供给到戊糖磷酸途径中，而来自脂类的能量主要来源于三酰甘油的脂肪分解。通过质谱成像技术，我们证明植物激素和磷脂的空间分布对胚胎发育有显著影响。我们还首次提供了紫杉中紫杉醇C的空间分布图谱。本研究的数据为跨多组学水平探索中药材紫杉种子萌发机制提供了基础。© 2023. Springer Nature Limited.

The transition from deep dormancy to seed germination is essential for the life cycle of plants, but how this process occurs in the gymnosperm Chinese yew (Taxus chinensis var mairei), the natural source of the anticancer drug paclitaxel, remains unclear. Herein, we analyse the transcriptome, proteome, spatial metabolome, and spatial lipidome of the Chinese yew and present the multi-omics profiles of dormant and germinating seeds. Our results show that abscisic acid and gibberellic acid 12 homoeostasis is closely associated with gene transcription and protein translation, and the balance between these phytohormones thereby determines if seeds remain dormant or germinate. We find that an energy supply of carbohydrates from glycolysis and the TCA cycle feed into the pentose phosphate pathway during seed germination, and energy supplied from lipids are mainly derived from the lipolysis of triacylglycerols. Using mass spectrometry imaging, we demonstrate that the spatial distribution of plant hormones and phospholipids has a remarkable influence on embryo development. We also provide an atlas of the spatial distribution of paclitaxel C in Chinese yew seeds for the first time. The data from this study enable exploration of the germination mechanism of Chinese yew seeds across several omics levels.© 2023. Springer Nature Limited.