Metabolomics Data Revealed Metabolite Changes during Endocarp Lignification in Kernel-Using Apricot

To understand the metabolite dynamics and genetic regulatory mechanism of apricot shell, a typical endocarp, before and after lignification are unknown, we investigated the metabolite differences of the endocarp of ‘Youyi,’ a popular kernel-using apricot cultivar, using ultra-performance liquid chromatography tandem mass spectrometry strategy. The endocarp thickness increased rapidly from 8 to 37 days after flowering (DAF) and lignin deposition began at 37 DAF. In total, 626 non-volatile metabolites were obtained from the endocarp tissues before (33 DAF) and after (41 and 45 DAF) lignification. The relative sugar and organic acid contents decreased continuously and those of L-phenylalanine and L-tyrosine increased after lignification. In the non-lignified endocarp, the phenylpropanoid metabolites were mainly in the form of p-coumaric acid, ferulic acid, neochlorogenic acid, dicumarol, coniferin, and some lignans. After lignification, the metabolites were mainly in the form of glycoside lignin or lactone coumarins, and the relative contents of L-asarinin and forsythin increased. The results of transcriptome confirmed the upregulation of genes related to lignin biosynthesis, including β-glucosidase and coniferyl-alcohol glucosyltransferase and laccases, accelerated lignification. This study provides insights into the formation of lignified endocarp in a kernel-using apricot and clarifies the role of monolignin transport and oxidative polymerization.