芍药是芍药科植物，是多年生草本花卉，具有重要的园艺价值。由于其在缓解疼痛、减轻炎症和免疫紊乱治疗方面的治疗应用，它在传统中医中占有重要地位。芍药苷是芍药中的活性单萜化合物，具有多种生物活性，例如抗炎和免疫调节作用。尽管芍药苷的药理作用已被广泛研究，但其生物合成途径仍然难以捉摸。在这里，我们结合了 PacBio Iso-Seq 和 RNA-seq 技术，研究了来自两种不同芍药生态型且芍药苷含量不同的三种不同组织。主要目的是鉴定参与芍药苷和相关单萜生物合成的候选基因。鉴定出差异表达的编码细胞色素P450、UDP-葡萄糖醛酸基和UDP-葡萄糖基转移酶以及转录因子的unigenes，这些基因可能与P.lactiflora中的单萜多样性有关。此外，我们还分析了两种P.lactiflora生态型之间的遗传分化。值得注意的是，与叶组织相比，根和根茎组织内萜烯途径的基因表达下调。这一有趣的观察使我们推测芍药苷的合成主要发生在叶子中，随后被转运到根部。然而，需要进一步的实验来提供实质性证据并验证这一假设。

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Paeonia lactiflora Pall., a Paeoniaceae family member, is a herbaceous perennial flower of significant horticultural importance. It holds prominence in traditional Chinese medicine due to its therapeutic applications in pain relief, inflammation reduction, and immune disorder treatment. Paeoniflorin, the active monoterpene compound in P. lactiflora, exhibits diverse biological activities, such as anti-inflammatory and immune-regulatory effects. Although the pharmacological effects of paeoniflorin have been extensively studied, its biosynthetic pathway remains elusive. Here, we combined PacBio Iso-Seq and RNA-seq techniques to investigate three distinct tissues from two different P. lactiflora ecotypes with varying paeoniflorin contents. The primary objective was to identify candidate genes involved in the biosynthesis of paeoniflorin and related monoterpenes. Differentially expressed unigenes encoding cytochrome P450s, UDP-glucoronosyl and UDP-glucosyl transferases, and transcription factors, which might be associated with monoterpene diversity in P. lactiflora, were identified. In addition, we analyzed genetic differentiation between the two P. lactiflora ecotypes. Notably, gene expression in the terpene pathway within root and rhizome tissues was downregulated compared to leaf tissues. This intriguing observation led us to speculate that paeoniflorin synthesis primarily occurs in the leaves and is subsequently transported to the roots. However, further experimentation is required to provide substantial evidence and verify this hypothesis.