## 5 Conclusions  
Agarwood, a resinous and fragrant wood, is highly valued for its use in medicine, perfumes, and incense across the world. The resinous stem of _Aquilaria sinensis_ (Lour.) Gilg is the sole legally authorized source of agarwood in China. However, whether other tissue parts can be potential substitutes for agarwood requires further investigation. To address this, we conducted metabolic analysis and transcriptome sequencing of six distinct tissues (root, stem, leaf, seed, husk, and callus) of _A. sinensis_ to investigate the variations in metabolite distribution characteristics and transcriptome data across different tissues. The volatile compound content was analyzed using chromatography-mass spectrometry (GC-MS), resulting in the identification of 331 differential metabolites through metabolomics analysis. Terpenoids constituted the majority of total metabolites (22.89%), with sesquiterpenes accounting for 51% of the identified terpenoids, predominantly distributed within the callus. The husk and leaf callus exhibited the highest degree of differential volatility, with a total of 229 distinct metabolite species identified. The RNA sequencing analysis revealed a significant enrichment of differentially expressed genes (DEGs) in the sesquiterpene synthesis pathway within the mevalonate pathway. The proportion of sesquiterpene synthase genes (60%) was significantly higher compared to other terpenoid synthase genes in callus. The transcriptional metabolic pattern demonstrated similarity between roots and stems. The present study provides comprehensive insights into the metabolome and transcriptome of _A. sinensis_, thereby establishing a solid foundation for future investigations on the biosynthesis and regulatory mechanisms underlying sesquiterpene production in _A. sinensis_, as well as potential alternatives to agarwood. The following supporting information can be downloaded at [[https://www.mdpi.com/article/10.3390/molecules29051075/s1](https://www.mdpi.com/article/10.3390/molecules29051075/s1)]([https://www.mdpi.com/article/10.3390/molecules29051075/s1](https://www.mdpi.com/article/10.3390/molecules29051075/s1)). Figure S1: The total ion current (TIC) of QC samples involves superimposing the ion flow diagram depicted in the figure; Figure S2: Orthogonal partial least squares-discriminant analysis (OPLS-DA) scores and OPLS-DA S-plot models between six different tissue sites; Figure S3: Bar Chart of DAMs between each comparison group (Top 20); Figure S4: KEGG enrichment of DAMs between each comparison group; Figure S5: Relative content of sesquiterpenes in six different tissue sites except for sesquiterpenes shown in Figure 5C; Figure S6: Volcano plot of differentially expressed genes among six different tissue sites; Figure S7: Enriched GO terms of DEGs between different control groups; Figure S8: Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of DEGs between different control groups; Figure S9: Nine quadrant diagram between different control groups; Table S1: Summary of 331 differential metabolites identified by GC-MS; Table S2: Ten subclasses of different volatile compounds in K-means cluster diagram. Conceptualization, L.H. and J.L. ; methodology, A.W. ; software, A.W. ; validation, A.W. and J.L. ; formal analysis, A.W. ; investigation, J.L. and A.W. ; resources, J.L. ; data curation, A.W. and J.L. ; writing--original draft preparation, A.W. ; writing--review and editing, J.L. ; visualization, A.W. ; supervision, J.L. ; project administration, J.L. and L.H. ; funding acquisition, J.L. and L.H. All authors have read and agreed to the published version of the manuscript. This research was supported by the Scientific and Technological Innovation Project of the China Academy of Chinese Medical Sciences (CI2023E002), the CACMS Innovation Fund (CI2021A04101), and the Fundamental Research Fund for the Central Public Welfare Research Institutes (ZZ13-YQ-093). The study did not require ethical approval. The study did not involve humans.