Quercus fabri is a common timber oak tree species widely distributed in subtropical areas of China. In this study, we presented a chromosome-scale reference genome assembly of Q. fabri achieved by integrating PacBio Sequel II, DNBseq™, and Hi-C sequencing platforms, and the results indicated the Q. fabri genome has a size of 836.74 Mb. Through the analysis of significantly expanded gene families, we identified that many of the top-ranked KEGG pathways are associated with amino acid metabolism. Subsequently, we performed an amino acid metabolic profile analysis on Q. fabri and related species, including Quercus aliena, Quercus acutissima, and Quercus variabilis. The findings revealed that the content of amino acids in Q. fabri was significantly higher than that in the other three oak species. Additionally, we found a significantly higher content of flavor amino acids, such as glutamic acid (Glu), aspartic acid (Asp), and glycine (Gly), in Q. fabri. Considering these results, we designed experiments to assess the nutrient content in mushrooms cultivated from the four oak trees. The results indicated that the total amino acid and protein content of mushrooms cultivated using Q. fabri as a substrate was significantly greater than that of mushrooms grown on the other three oak species. This characteristic may explain why Q. fabri wood is particularly effective as a substrate for cultivating more flavorful mushrooms. This study presents the complete genome and evolutionary information of Q. fabri, and integrates metabolic profiling to explore the underlying reasons for the enhanced flavor of mushrooms cultivated from it.

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