Dynamic Transcriptomics Unveils Parallel Transcriptional Regulation in Artemisinin and Phenylpropanoid Biosynthesis Pathways under Cold Stress in Artemisia annua

Abstract Cold stress, a major abiotic factor, positively modulates the synthesis of artemisinin in Artemisia annua (A. annua) and influences the biosynthesis of other secondary metabolites. To elucidate the flux changes in the synthesis of secondary metabolites under low-temperature conditions, we conducted dynamic transcriptomic and metabolite quantification analyses of A. annua leaves. The accumulation of total organic carbon (TOC) in leaves under cold stress provided ample precursors for secondary metabolite synthesis. Short-term exposure to low temperature induced a transient increase in jasmonic acid synthesis, which positively regulates the artemisinin biosynthetic pathway, contributing to artemisinin accumulation. Additionally, transcripts of genes encoding key enzymes and transcription factors in both the phenylpropanoid and artemisinin biosynthetic pathways, including PAL, F3'H, ADS, and DBR2, exhibited similar expression patterns, suggesting a synergistic effect between these pathways. Prolonged exposure to low temperature sustained high levels of phenylpropanoid synthesis, leading to significant increases in lignin, flavonoids, and anthocyanin. Conversely, the final stage of the artemisinin biosynthetic pathway is inhibited under these conditions, resulting in elevated levels of dihydroartemisininic acid and artemisininic acid. Collectively, our study provides insights into the parallel transcriptional regulation and metabolic flux of artemisinin and phenylpropanoid biosynthetic pathways in A. annua under cold stress.