Transcriptomic Analysis Reveals the Mechanism of Lignin Biosynthesis in Fresh-Cut Cucumber

When subjected to a certain degree of mechanical damages, a systematic responsive mechanism of fresh-cut cucumber is activated. Among them, the lignin produced in the secondary metabolism will make the fresh-cut cucumber lignified, which will increase the hardness and whiten the cutting surface of the fresh-cut cucumber, seriously affecting the taste and appearance quality. In order to further understand the mechanism of lignin synthesis, transcriptome analysis was carried out on two cutting types of fruit samples from the slices treatment (P) and shreds treatment (S) stored for 24 h. Compared with the whole fruit (CK), 2281 and 2259 differentially expressed genes (EDGs) were identified in the slices and shreds treatments, respectively; 1442 up-regulated genes and 839 down-regulated genes were expressed as 2281 in the slices treatment; 1475 significantly up-regulated genes and 784 significantly down-regulated genes were expressed as 2259 in the shreds treatment; and 1582 DEGs were commonly detected between the slices treatment and shreds treatment, indicating that these DEGs were related to lignin synthesis. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that compared with the whole fruit, the metabolic pathways of amino acid metabolism, lipid metabolism, and secondary metabolism were affected by mechanical damages. This study revealed that JA biosynthesis was activated by mechanical damages, and the up-regulation of phenylalanine metabolism and phenylalanine, tyrosine, and tryptophan metabolism affected phenylpropanoid biosynthesis, which may promote lignin synthesis. Fifteen DEGs were selected for qRT-PCR validation, and the reliability and accuracy of transcriptome data were confirmed.