Metabolome and transcriptome analyses reveal metabolic differences and identify candidate regulatory factors among three habitat types of Gentiana scabra Bunge

Introduction Gentiana scabra Bunge, a primary botanical source of the traditional Chinese medicine Gentianae Radix et Rhizoma . The quality of G. scabra varies under different habitats, but the underlying mechanism remains unclear. Methods In this study, comparative analyses of UPLC-MS/MS-based metabolomics and RNA-seq-based transcriptomics were integrated to reveal differences in metabolite accumulation among G. scabra grown in three habitats: wild shrublands, wild meadows, and cultivated farmlands. Results A total of 1824 metabolites and 93076 Unigenes were identified across G. scabra from the three habitats. Specifically, 309 differential metabolites (DMs) and 645 differentially expressed genes (DEGs) were detected between the wild meadow group (YC) and wild shrubland group (YG), while 348 DMs and 605 DEGs were observed between the cultivated farmland group (ZP) and wild meadow group (YC).A total of 510 DMs and 917 DEGs were identified between the cultivated farmland group (ZP) and wild shrubland group (YG), which reveals differences in metabolite accumulation of G. scabra among the three habitats. Integrated analysis further identified genes associated with the quality formation of G. scabra medicinal materials, and these genes play crucial roles in the accumulation of metabolic compounds in G. scabra . Genes such as 3-hydroxy-3-methylglutaryl-CoA reductase ( HMGR ), diphosphomevalonate decarboxylase ( MVD ), and isopentenyl diphosphate isomerase ( IDI ) may be involved in regulating terpenoid backbone biosynthesis. Discussion DMs were mainly enriched in “metabolic pathways” and “environmental information processing”, which may be attributed to the effects of environmental factors in the growing habitats of G. scabra . The expression levels of four genes, namely HSFF, SCPL-I, LOC107801770 , and CYP71D55 , can serve as candidate genes for distinguishing G. scabra from the three habitats. This study provides a theoretical basis for future molecular breeding and “simulative habitat cultivation” of G. scabra .