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Objective:Lilium brownii var.viridulum(LB)and L.lancifolium(LL)are the main sources of medicinal lily(Lilii Bulbus,Baihe in Chinese)in China.However,the functional components of these two species respon-sible for the treatment efficacy are yet not clear.In order to explore the therapeutic material basis of Lilii Bulbus,we selected L.davidii var.willmottiae(LD)only used for food as the control group to analyze the differences between LD and the other two(LB and LL).Methods:Metabolome and transcriptome were carried out to investigate the differences of active com-ponents in LD vs LB and LD vs LL.Data of metabolome and transcriptome was analysed using various analysis methods,such as principal component analysis(PCA),hierarchical cluster analysis(HCA),and so on.Differentially expressed genes(DEGs)were enriched through KEGG and GO enrichment analysis.Results:The PCA and HCA of the metabolome indicated the metabolites were clearly separated and varied greatly in LL and LB contrasted with LD.There were 318 significantly differential metabolites(SDMs)in LD vs LB group and 298 SDMs in LD vs LL group.Compared with LD group,the significant up-regulation of steroidal saponins and steroidal alkaloids were detected both in LB and LL groups,especially in LB group.The HCA of transcriptome indicated that there was significant difference in LB vs LD group,while the dif-ference between LL and LD varied slightly.Additionally,47 540 DEGs in LD vs LB group and 18 958 DEGs in LD vs LL group were identified.Notably,CYP450s involving in the biosynthesis of steroidal saponins and steroidal alkaloids were detected,and comparing with LD,CYP724,CYP710A,and CYP734A1 in LB and CYP90B in LL were all up-regulated.Conclusion:This study suggested that steroidal saponins and steroidal alkaloids maybe the representa-tive functional components of Lilii Bulbus,which can provide new insights for Lilii Bulbus used in the research and development of classic famous formula.