A Regulatory Network Revealing Spatial Distribution Differences of Alkaloids, Flavones, and Carbohydrates in Fritillaria thunbergii Bulbs by Multi-omics Analysis

The secondary metabolites in the bulbs of Fritillaria species display distinct spatial distribution patterns, yet the underlying mechanisms remain unclear. In this study, bulbs of Fritillaria thunbergii were divided into inside (IS) and outside (OS) layers. Integrated physiological, transcriptomic, metabolomic, and microbiomic analyses were performed to elucidate the spatial regulation of alkaloids, flavonoids, and carbohydrates. The OS was significantly enriched in secondary metabolites, with total alkaloid, peimine, and total flavonoid contents being approximately 1.18-, 1.28-, and 1.24-fold higher, respectively, than those in the IS. In contrast, carbohydrates mainly accumulated in the IS, where sucrose and starch levels were 1.37- and 2.18-fold higher than those in the OS. Transcriptomic analysis revealed that carbohydrate enrichment in the IS was associated with the upregulation of sucrose synthase ( SUS ) and hexokinase ( HK ) genes, and the downregulation of β-amylase3 ( BAM3 ) and invertase ( INV ). In the OS, genes related to steroidal alkaloid biosynthesis, including 3-hydroxy-3-methylglutaryl-CoA synthase ( HMGCS ), 1-deoxy-D-xylulose-5-phosphate reductoisomerase ( DXR ), and farnesyl-diphosphate farnesyltransferase 1 ( FDFT1 ), as well as flavonoid biosynthesis genes phenylalanine ammonia-lyase ( PAL ), 4-coumarate-CoA ligase ( 4CL ), and cytochrome P450 monooxygenase CYP75B1 ( CYP75B1 ), were upregulated. Moreover, bacterial taxa enriched in the OS, such as Actinomycetota and Ruminococcus , correlated positively with alkaloid accumulation, while the fungal genus Aspergillus was potentially associated with flavonoid regulation. Overall, the multi-omics insights provided here not only offer theoretical support for refined, region-specific processing of Zhejiang Fritillaria bulbs but also open new avenues to improve medicinal quality by manipulating host gene expression and microbial community composition. • Outside layer accumulates alkaloids (peimine 1.28×) and flavonoids (1.24×) vs inside. • Inside layer is enriched in carbohydrates: sucrose 3.7× and starch 11.5× vs outside. • Inside layer upregulates SUS and HK, and represses BAM3 to sustain sugar storage. • Bulb outside layer highly expresses alkaloid and flavonoid biosynthesis genes. • Outside layer microbes associate with elevated alkaloid and flavonoid levels.