biostudies-literatureUnknown13Duan Y<i>Fritillaria hupehensis</i>, a well-known medicinal perennial herb, is used as an antitussive and an expectorant. Continuous cropping and monoculture cultivation usually negativly affect the growth of <i>F. hupehensis</i>. Compared with the monoculture system, the <i>F. hupehensis</i>-<i>Magnolia officinalis</i> intercropping system significantly increases the yield of <i>F. hupehensis</i>. However, changes in steroidal alkaloid metabolites (the most important bioactive components) and their molecular regulatory mechanisms in <i>F. hupehensis</i> intercropping system remain unclear. We performed comparative transcriptomic and metabolomic analyses of <i>F. hupehensis</i> bulbs grown in monocropping and intercropping systems. A total of 40 alkaloids were identified, including 26 steroidal Frontiers in plant science997868https://www.ebi.ac.uk/biostudies/studies/S-EPMC9585282biostudies-literatureTranscriptomic and metabolic analyses reveal the potential mechanism of increasing steroidal alkaloids in <i>Fritillaria hupehensis</i> through intercropping with <i>Magnolia officinalis</i>.PMC9585282Liu XWu JYou JGuo JGuo XWang FTang TLiao MDuan YfalseTranscriptomic and metabolic analyses reveal the potential mechanism of increasing steroidal alkaloids in <i>Fritillaria hupehensis</i> through intercropping with <i>Magnolia officinalis</i>.<i>Fritillaria hupehensis</i>, a well-known medicinal perennial herb, is used as an antitussive and an expectorant. Continuous cropping and monoculture cultivation usually negativly affect the growth of <i>F. hupehensis</i>. Compared with the monoculture system, the <i>F. hupehensis</i>-<i>Magnolia officinalis</i> intercropping system significantly increases the yield of <i>F. hupehensis</i>. However, changes in steroidal alkaloid metabolites (the most important bioactive components) and their molecular regulatory mechanisms in <i>F. hupehensis</i> intercropping system remain unclear. We performed comparative transcriptomic and metabolomic analyses of <i>F. hupehensis</i> bulbs grown in monocropping and intercropping systems. A total of 40 alkaloids were identified, including 26 steroidal 2022-01-01T00:00:00Z20222025-04-26T00:50:45.329Z2025-04-06T09:55:22.371ZS-EPMC95852823627550810.3389/fpls.2022.997868