Macadamia ternifolia is a valuable oil-producing nut crop in the world. The husk is frequently regarded as a low-grade material because the metabolic profile of the husk is still unknown. In order to explore the industrial significance of husk, this study performed metabolic and transcriptomic analyses at various development stages of the husk. The qualitative and quantitative metabolic data analysis identified 596 metabolic substances including several species of phenolic acids, flavonoids, lipids, organic acids, amino acids and derivatives, nucleotides and derivatives, alkaloids, lignans, and coumarins, terpenoids, tannins, and others. However, phenolic acids and flavonoids were predominant and their abundance levels were significantly altered across different development stages of the husk. Comparative transcriptome analysis revealed that expression patterns of phenolic acid and flavonoid pathway genes were significantly changed with husk growth. In particular, the expression of PAL, C4H, 4CL, CHS, CHI, F3H, and FLS had dynamic differences at various development stages of the husk. Our integrative metabolomic and transcriptomic analyses identified key metabolic substances, characterized their abundance level, and further discussed the regulatory mechanism of phenolic and flavonoid biosynthesis in the husk of M. ternifolia. Our results provide new insight into biological profiles of the husk of M. ternifolia and help to elucidate the molecular mechanisms of phenolic and flavonoid biosynthesis in the husk of M. ternifolia for a better valorization.
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