Transcriptomics and metabolomics reveal the primary and secondary metabolism changes in with different forms of nitrogen utilization.

The roots and rhizomes of Fisch. represent the oldest and most frequently used herbal medicines in Eastern and Western countries. However, the quality of cultivated has not been adequate to meet the market demand, thereby exerting increased pressure on wild populations. Nitrogen, vital for plant growth, potentially influences the bioactive constituents of plants. Yet, more information is needed regarding the effect of different forms of nitrogen on . seedlings were exposed to a modified Hoagland nutrient solution (HNS), varying concentrations of nitrate (KNO), or ammonium (NH)SO. We subsequently obtained the roots of for physiology, transcriptomics, and metabolomics analyses. Our results indicated that medium-level ammonium nitrogen was more effective in promoting growth compared to nitrate nitrogen. However, low-level nitrate nitrogen distinctly accelerated the accumulation of flavonoid ingredients. Illumina sequencing of cDNA libraries prepared from four groups-treated independently with low/medium NH or NO identified 364, 96, 103, and 64 differentially expressed genes (DEGs) in each group. Our investigation revealed a general molecular and physiological metabolism stimulation under exclusive NH or NO conditions. This included nitrogen absorption and assimilation, glycolysis, Tricarboxylic acid (TCA) cycle, flavonoid, and triterpenoid metabolism. By creating and combining putative biosynthesis networks of nitrogen metabolism, flavonoids, and triterpenoids with related structural DEGs, we observed a positive correlation between the expression trend of DEGs and flavonoid accumulation. Notably, treatments with low-level NH or medium-level NO positively improved primary metabolism, including amino acids, TCA cycle, and glycolysis metabolism. Meanwhile, low-level NH and NO treatment positively regulated secondary metabolism, especially the biosynthesis of flavonoids in . Our study lays the foundation for a comprehensive analysis of molecular responses to varied nitrogen forms in , which should help understand the relationships between responsive genes and subsequent metabolic reactions. Furthermore, our results provide new insights into the fundamental mechanisms underlying the treatment of and other plants with different nitrogen forms.