Uncovering the genetic basis for enhanced mushroom flavor in Quercus fabri through genome sequencing and metabolic profiling

Abstract

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.

Acknowledgements

This work was supported by the Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural Varieties (2021C02070-9) and the National Key R&D Program of China (2023YFD2200602).

Author contributions

L.W.W. and Y.D.W. conceived and designed the experiments. L.W.W., Y.Q.C., and X.S. were involved in the plant material preparation and extraction. L.W.W., Y.Q.C., S.F.X., and Y.C.C. performed genotyping, genomic, and statistical analysis. L.W.W. and C.G.J. performed the detection of amino acid metabolic profile, culture of mushrooms, and determination of total amino acid and protein content. L.W.W. and Y.Q.C. wrote the draft of the manuscript. C.G.J., X.S., S.F.X., and Y.C.C. assisted in data analysis. All authors have edited, reviewed, and approved the manuscript.

Data availability

The raw data of genome sequencing of Quercus fabri is deposited in the NCBI SRA database with BioProject ID PRJNA1189174. The data, such as the assembled genome sequence, gene function annotation, repetitive sequences, predicted CDS, protein sequences, transcriptional factor, and amino acid metabolic profile, are available at FigShare (https://doi.org/10.6084/m9.figshare.27927681).

Conflict of interest statement

The authors declare that they have no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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