Integrated transcriptomic and metabolomic analyses reveal sodium selenite-induced molecular responses and metabolic remodeling in Stemona tuberosa roots.

Selenium (Se) is a bioactive trace element that influences plant growth, development, and metabolic processes. However, the molecular and metabolic responses of medicinal plants to exogenous sodium selenite remain poorly understood. In this study, Stemona tuberosa Lour. roots were treated with 20 mg/L sodium selenite (Na2SeO3) for 40 days, and integrated transcriptomic and metabolomic analyses were performed to characterize Se-responsive changes. The results revealed substantial transcriptional and metabolic changes in response to Na2SeO3 treatment. Metabolomic analysis identified 669 differentially accumulated metabolites (DAMs), predominantly involving amino acids and derivatives, organic acids, carbohydrates, lipids, and secondary metabolism-related compounds. KEGG enrichment analysis showed that DAMs were mainly associated with metabolic pathways, amino acid biosynthesis, nucleotide metabolism, inositol phosphate metabolism, and secondary metabolite biosynthesis. Transcriptomic analysis identified 16,577 differentially expressed genes (DEGs), including 9,134 upregulated and 7,443 downregulated genes. These DEGs were mainly enriched in metabolic processes, stimulus responses, plant hormone signal transduction, phenylpropanoid biosynthesis, flavonoid biosynthesis, and starch and sucrose metabolism. Transcription factor analysis indicated that AP2/ERF, MYB, WRKY, bHLH, and NAC families were prominently represented among Se-responsive transcription factors. Integrated analyses identified coordinated associations among genes, transcription factors, and metabolites, suggesting that these coordinated molecular patterns may be associated with the response of S. tuberosa roots to Na2SeO3. Overall, this study provides insights into the molecular and metabolic changes associated with Na2SeO3 exposure in medicinal plants.