After A. mellea colonizes G. elata, fungal growth is restricted to its cortex layer (Fig. 3c, Supplemental Fig. 14). We performed a tissue-specific qPCR-based analysis of 10 genes in G. elata tubers and found that PDR transcripts, which mediate secretion of strigolactone to the extracellular space, were highly abundant in the cortex layer (Supplementary Fig. 15). This finding suggests that G. elata may preferentially guide A. mellea to colonize its cortex layer. Similarly to ATP synthases, we found that some glycoside hydrolases from gene families that have expanded in the G. elata genome were also highly expressed in the cortex layer, supporting the idea that A. mellea hyphal walls are digested in the cortex layer of G. elata tubers (Supplementary Table 39). The expanded endo-β-1,4-d-xylanase and β-glucosidase may have become neofunctionalized to cleave fungal glycan substrates during the digestion of hyphal walls of A. mellea (Fig. 3a, Supplementary Table 40)26,27.