Time-resolved transcriptomics reveals ABA-related regulation and phenylpropanoid responses in Herpetospermum...

Salt stress is a major abiotic factor limiting plant growth and productivity. Herpetospermum pedunculosum, a medicinal plant adapted to high-altitude environments, offers a unique non-model system for investigating salt stress responses. Here, we combined physiological and biochemical assays with time-course root transcriptome profiling to characterize the responses of H. pedunculosum to 200 mM NaCl treatment. Salt stress induced rapid wilting, oxidative stress-related physiological changes, membrane damage, and significant accumulation of ABA, total lignin, and total lignans. RNA-seq across five time points (1, 3, 24, 48, and 96 h) identified nearly 28,000 differentially expressed genes (DEGs), which formed distinct temporal clusters associated with hormone signaling, transcriptional regulation, stress responses, and phenylpropanoid-related metabolism. Antioxidant enzyme-related genes, ABA biosynthesis/homeostasis genes, ABA signaling components, and lignin/lignan pathway biosynthesis genes (LLPBGs) showed stage-specific expression patterns, with several genes responding rapidly during the early phase of salt stress. WGCNA and co-expression analyses further identified trait-associated modules and candidate links among core TFs, ABA-related genes, and LLPBGs. Subcellular localization, yeast transactivation, Y1H and Dual-LUC assays provided preliminary evidence that the AP2/ERF factor HpERF141 can bind to and activate the promoter of the previously characterized lignan-related gene HpDIR17. Overall, this study provides a root-focused transcriptomic resource and identifies candidate regulatory genes potentially linking ABA-related responses with lignin/lignan-associated metabolism in H. pedunculosum under salt stress.