Abstract:Truffles must be symbiotic with plants to form ectomycorrhiza (ECM), which facilitates the formation of fruiting bodies by mutually beneficial exchanges of substances. [Objective] To elucidate the flow of substances between Tuber sinense and Pinus yunnanensis in a symbiosis relationship. [Methods] Liquid chromatography-mass spectrometry (LC-MS) was employed to analyze the metabolite profiles of freshly harvested T. sinense (SL) and P. yunnanensis roots (SG). [Results] In SL and SG, 1 304 and 1 516 substances were detected respectively, including 399 SL-specific substances (SLSs) and 611 SG-specific substances (SGSs). There were 294 common differential substances, including 93 up-regulated substances (DEMs-up) and 201 down-regulated substances in SL. The network correlation analysis revealed that 92 of the 100 substances with the relative content ≥2.0 (40 SLSs and SGSs and 60 DEMs-up) displayed significant correlations. Twenty-nine associated substances in SLSs and SGSs and 19 substances in DEMs-up were enriched in 15 important pathways, which mainly involved secondary metabolite biosynthesis, amino acid biosynthesis and metabolism, and vitamin biosynthesis and metabolism. [Conclusion] A network correlation existed between T. sinense and P. yunnanensis pine roots metabolites. Some substances in truffles and pine roots, including adenosine 3',5'-cyclic monophosphate (cAMP), phytosterol, and indole-3-acetic acid, had regulatory effects on the development of fruiting bodies. The findings provided a theoretical basis for further studying the potential signaling molecules associated with fruiting body development and elucidating the symbiotic mechanism between T. sinense and pines. Additionally, this study laid a practical basis for screening the substances promoting the growth of mycorrhizal seedlings and fruiting bodies and for large-scale artificial cultivation of truffles.