Comprehensive analysis of the transcriptomics and metabolomics reveal the changes induced by nano‐selenium and melatonin in Zizyphus jujuba Mill. cv. Huizao

Abstract BACKGROUND Jujube ( Zizyphus jujuba ), belonging to the Rhamnaceae, contains various bioactive components including flavonoids and polysaccharides. In our previous study, jujube quality was improved by application of nano‐selenium (Nano‐Se) and melatonin; however, little research has been conducted on the induced molecular mechanisms. Zizyphus jujuba cv. Huizao was used as experimental materials to compare and analyze the transcriptomics and metabolomics mechanisms. RESULTS Compared with the control, 305, 422, and 240 metabolites and 24, 281, and 44 genes were significantly changed at the metabolic and transcriptional levels in Nano‐Se, melatonin, and Nano‐Se with melatonin treatments, respectively. The metabolomics indicated that the differentially expressed metabolites were involved in phenylpropanoid biosynthesis, fructose, and mannose metabolic pathways. The Nano‐Se with melatonin treatment group increased the contents of glucose and total Se by 1.8 and 5.4 times, respectively. Transcriptomics showed that differentially expressed genes of Nano‐Se and melatonin treatment were mainly enriched in phenylpropanoid biosynthesis, pentose, and glucuronate interconversions pathways. In addition, several transcription factors from the NAC, WRKY, MYB, and WRKY families were identified in melatonin versus control and melatonin versus Nano‐Se. Furthermore, combined transcriptomic and metabolomic analysis showed that phenylpropanoid biosynthesis, starch and sucrose metabolism, the mutual conversion pathway of pentose, and glucuronate interconversions were the vital pathways in response to Nano‐Se and melatonin treatment. CONCLUSION Overall, these results provide new insights into jujube response to Nano‐Se and melatonin, and improve our understanding of the jujube molecular mechanisms induced by Nano‐Se and melatonin. © 2025 Society of Chemical Industry.