Comprehensive Metabolomic–Transcriptomic Analysis of the Regulatory Effects of Armillaria mellea Source Differences on Secondary Metabolism in Gastrodia elata

<i>Armillaria mellea</i> (<i>A. mellea</i>) serves as a crucial nutritional source for <i>Gastrodia elata</i> (GE) growth, and its origin directly influences the GE quality and yield. This study analyzed GE symbiotic with <i>A. mellea</i> from different sources using metabolomics and transcriptomics. Results demonstrated that Group A exhibited significant differences in metabolites and gene expression compared to other groups. Group A showed significantly higher accumulation of active components like gastrodin and p-hydroxybenzyl alcohol than others, but its yield was lower than Group B. Metabolomic analysis identified 2418 metabolites, while transcriptomic sequencing produced 964,110,904 clean reads, with 14,637 annotated transcripts. KEGG analysis revealed that Group A's DEGs and DEMs were co-enriched in three key pathways, including flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction, such as the positive regulatory roles of key genes (<i>CHS</i>, <i>4CL</i>, <i>MYC2</i>) on metabolites such as hesperetin, ferulate, and jasmonic acid, respectively. The coordinated upregulation of gene-metabolite interactions in Group A GE may be closely related to the accumulation of major active components, indirectly suggesting the influence of the <i>A. mellea</i> source on metabolic and transcriptional response differences in GE. This study, centered on the host GE, indirectly deduces the association between <i>A. mellea</i> and GE, providing a theoretical basis for screening high-quality "fungus-GE" combinations. Further in-depth research and validation experiments will be conducted in conjunction with fungal omics.