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

## TL;DR

This study explores how different sources of Armillaria mellea affect the secondary metabolism and quality of Gastrodia elata through metabolomic and transcriptomic analysis.

## Contribution

The study identifies specific genes and metabolites influenced by different Armillaria mellea sources, offering insights for optimizing Gastrodia elata cultivation.

## Key findings

- Group A Armillaria mellea promotes accumulation of active components like gastrodin but lowers yield.
- Group B Armillaria mellea is associated with higher yield but lower accumulation of beneficial metabolites.
- Key genes like CHS and 4CL are linked to metabolite pathways in Gastrodia elata.

## Abstract

Gastrodia elata, as a plant with dual purposes for medicine and food, has garnered significant attention. However, the formation of its quality and yield is influenced by differences in the sources of Armillaria mellea. This study aims to reveal the varying effects of Armillaria mellea from different sources on the secondary metabolism of co-cultivated Gastrodia elata, which holds substantial implications for the Gastrodia elata cultivation industry. Centered on the host (Gastrodia elata), the study indirectly deduced that Armillaria mellea A may induce the upregulation of numerous metabolites and genes in Gastrodia elata, thereby promoting the accumulation of beneficial components, while Armillaria mellea B might be more conducive to enhancing the yield. The co-enrichment pathway analysis of flavonoids, phenylpropanoids, and plant hormone signal transduction identified multiple key regulatory genes (such as CHS and 4CL) and key metabolites (such as hesperetin and ferulate) in Gastrodia elata. Our findings provide important insights for the next steps in screening and validating high-quality regulatory genes. Based on these conclusions, further in-depth research will be conducted in combination with a fungal omics analysis, with the aim of providing molecular evidence for constructing efficient “fungus-Gastrodia” combinations.

Armillaria mellea (A. mellea) serves as a crucial nutritional source for Gastrodia elata (GE) growth, and its origin directly influences the GE quality and yield. This study analyzed GE symbiotic with A. mellea 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 (CHS, 4CL, MYC2) 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 A. mellea source on metabolic and transcriptional response differences in GE. This study, centered on the host GE, indirectly deduces the association between A. mellea 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.