Data Sheet 1_Integrated metabolomic and transcriptomic profiling elucidates the tissue-specific biosynthesis and regulation of flavonoids in Machilus nanmu.docx

IntroductionMachilus nanmu is a significant arborescent species of the genus Machilus (Lauraceae), exhibiting considerable potential for applications in industrial materials and healthcare. However, systematic investigations into its flavonoid metabolites and associated biosynthetic mechanisms remain limited, which significantly hinders the efficient exploitation and sustainable utilization of this species.
MethodsThis multi-omics study revealed the specific accumulation pattern of flavonoids in the tissues of M. nanmu and pinpointed key structural and regulatory genes underlying their biosynthesis by integrating widely targeted metabolomics and transcriptomics data from roots, stems, and leaves.
ResultsA total of 425 flavonoid compounds and 35,671 differentially expressed genes were detected. Further screening revealed 41 structural genes encoding 19 key enzymes (including PAL, CHS, FLS, UGTs, etc.), among which two UGTs (Cluster-69292 and Cluster-71935) were subcellularly localized to the cytoplasm. Furthermore, the weighted gene co-expression network analysis (WGCNA) revealed four key modules exhibiting strong correlations with flavonoid content. From these modules, four core transcription factors (TFs) from the MYB and bHLH families were identified as putative regulators of flavonoid biosynthesis.
DiscussionOur findings offer the first comprehensive model of tissue-specific flavonoid accumulation in M. nanmu, enabling the dissection of its transcriptional machinery and advancing strategies for its genetic improvement and resource exploitation.

引言
楠木（Machilus nanmu）是樟科润楠属重要乔木树种，在工业材料与医疗健康领域具有极高应用潜力。然而，目前针对其黄酮类代谢物及相关生物合成机制的系统性研究仍较为匮乏，这极大阻碍了该树种的高效开发与可持续利用。

研究方法
本多组学研究整合了楠木根、茎、叶的广泛靶向代谢组学（widely targeted metabolomics）与转录组学（transcriptomics）数据，揭示了其组织特异性黄酮类化合物积累模式，并精准定位了黄酮类生物合成相关的关键结构基因与调控基因。

结果
本研究共检测到425种黄酮类化合物以及35671个差异表达基因。进一步筛选得到41个结构基因，编码19种关键酶（包括苯丙氨酸解氨酶（PAL）、查尔酮合酶（CHS）、黄酮醇合酶（FLS）、糖基转移酶（UGTs）等），其中2个UGTs基因（Cluster-69292与Cluster-71935）被亚细胞定位于细胞质中。此外，加权基因共表达网络分析（WGCNA）结果显示，有4个关键模块与黄酮类化合物含量呈显著相关。从这些模块中，我们鉴定出4个来自MYB与bHLH家族的核心转录因子（TFs），推测其为黄酮类生物合成的调控因子。

讨论
本研究首次构建了楠木组织特异性黄酮类化合物积累的完整模型，为解析其转录调控机制、推进该树种的遗传改良与资源开发策略提供了重要支撑。