We next explored how gene expansion in G. elata may have contributed to its association and interactions with fungal microbiota. The monocot mannose-binding lectin antifungal protein family (GAFP) of G. elata contains 20 genes, compared to only 3 in A. comosus and 0 in A. thaliana (Supplementary Table 27). GAFP proteins have been documented to inhibit the growth of both ascomycete and basidiomycete fungal plant pathogens in vitro20. More than 80% of the GAFP genes were highly expressed in protocorms and juvenile tubers, the growth stages that occur before G. elata establishes a stable symbiotic association with A. mellea (Fig. 2c). 4-Hydroxybenzyl alcohol (p-PA), the precursor of the phytoalexin gastrodin is a major phenolic compound of G. elata21. The expression of p-PA biosynthesis genes (e.g., cinnamate 4-hydroxylase, C4H, alcohol dehydrogenase, ADH, hydroxybenzaldehyde synthase, HBS)21 was relatively high in protocorms and juvenile tubers. Ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS) metabolite analysis revealed that p-HA is present in G. elata tubers but not in A. mellea hyphae (sampled from tuber, wood, and PDA medium). S-(p-HA)-glutathione was detected in both G. elata tubers and in A. mellea hyphae sampled from tubers (Supplementary Fig. 12, Supplementary Table 35), which putatively suggests that G. elata may transport this phytoalexin to A. mellea and prevent the excessive growth of A. mellea. To investigate the effect of A. mellea on microbial management in G. elata, we performed a 16S ribosomal (rRNA) and rDNA ITS sequencing analysis and found that the diversity of bacterial and microbial species was significantly lower during the protocorm stage than at other growth stages (p < 0.05), which was consistent with the pattern of gene expression of GAFP (Fig. 2c, d, Supplementary Tables 36, 37). This increased diversity of bacteria and fungi during the juvenile tuber to mature tuber periods implies that a compatible mycorrhizal fungus (A. mellea) can affect the structure of the microbial community associated with its host and greatly reduce the antifungal and antibacterial activities as a symbiotic association with A. mellea is established.