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Background   Anoectochilus roxburghii  is a traditional Chinese medicine with potent medicinal activity owing to the presence of secondary metabolites, particularly flavonoids.  A. roxburghii  also maintains a symbiotic relationship with mycorrhizal fungi. Moreover, mycorrhizal fungi can induce metabolite synthesis in host plants. However, little is known about the role of mycorrhizal fungi in promoting the accumulation of flavonoid metabolites in  A. roxburghii .    Methods   A. roxburghii  and the isolated fungus  Ceratobasidium  sp. AR2 were cocultured. The portion of  A. roxburghii  above the medium treated with or without AR2 was studied by transcriptome and target metabolome analyses.    Results  AR2 promoted the growth and development of  A. roxburghii . The contents of total flavonoid, rutin, isorhamnetin, and cyanidin-3-glucoside chloride were increased compared with those in uninoculated cultures. Transcriptome analysis suggested that 109 unigenes encoding key enzymes were potentially associated with changes in flavonoids. Quantitative real-time polymerase chain reaction of fourteen flavonoid-related unigenes showed that most flavonoid biosynthetic genes were significantly differentially expressed between inoculated and uninoculated plantlets.    Conclusion  The isolate AR2 could significantly promote the growth and development of  A. roxburghii  and the accumulation of flavonoids. Overall, our findings highlighted the molecular basis of the effects of mycorrhizal fungi on flavonoid biosynthesis in  A. roxburghii  and provided novel insights into methods to improve the yield and quality of  A. roxburghii .

Effects of the mycorrhizal fungus Ceratobasidium sp. AR2 on growth and flavonoid accumulation in Anoectochilus roxburghii