AbstractBackgroundPanax quinquefolius L. is one of the most important foods and herbs because of its high nutritional value and medicinal potential. In our previous study we found that the ginsenoside content in P. quinquefolius was improved by arbuscular mycorrhizal fungi (AMFs). However, little research has been conducted on the molecular mechanisms in P. quinquefolius roots induced by AMFs colonization. To identify the metabolomic and transcriptomic mechanisms of P. quinquefolius induced by AMFs, non‐mycorrhized (control) and mycorrhized (AMF) P. quinquefolius were used as experimental materials for comparative analysis of the transcriptome and metabolome.ResultsCompared with the control, 182 metabolites and 545 genes were significantly changed at the metabolic and transcriptional levels in AMFs treatment. The metabolic pattern of AMFs was changed, and the contents of ginsenosides (Rb1, Rg2), threonine, and glutaric acid were significantly increased. There were significant differences in the expression of genes involved in plant hormone signal transduction, glutathione metabolism, and the plant–pathogen interaction pathway. In addition, several transcription factors from the NAC, WRKY, and basic helix–loop–helix families were identified in AMFs versus the control. Furthermore, the combined analysis of ‘transcriptomics–metabolomics’ analysis showed that ‘Plant hormone signal transduction’, ‘Amino sugar and nucleotide sugar metabolism’ and ‘Glutathione metabolism’ pathways were the important enriched pathways in response to AMFs colonization.ConclusionOverall, these results provide new insights into P. quinquefolius response to AMFs, which improve our understanding of the molecular mechanisms of P. quinquefolius induced by AMFs. © 2023 Society of Chemical Industry.