Multi-Omics Dissection Reveals the Central Regulator NtHY5 Rewires Primary and Secondary Metabolism to Strengthen Biotic and Abiotic Stress Defences in Nicotiana Tabacum.

ALKBH10B mediated epitranscriptomic regulation enhances drought tolerance of Arabidopsis thaliana via hormonal cross-talk and sustained photosynthesis

The results suggest that ALKBH10B enhances drought tolerance by coordinating m⁶A-dependent transcriptional and post-transcriptional regulation to maintain photosynthetic capacity and mitochondrial energy metabolism, as well as fine-tuning ABA-jasmonate crosstalk.

The R2R3-MYB transcription factor ScMYB20 negatively regulates drought and salt tolerance through a dual-repression of ScCHALCONE SYNTHASE-1 (ScCHS1)-mediated flavonoid biosynthesis in the desert moss Syntrichia caninervis.

Genome-wide analysis of AP2/ERF genes identifies HpERF144 as a regulator of salt tolerance and phenylpropanoid metabolism in Herpetospermum pedunculosum.

Findings identify HpERF144 as a link between salt stress signaling and phenylpropanoid-associated metabolic regulation in a lignan-rich medicinal plant.

Transcriptomic Analysis Reveals the Molecular Mechanisms Underlying Heat-Induced Suppression of Polymethoxyflavone Accumulation in Citrus Leaves

High-temperature stress impairs plant growth and alters secondary metabolism. Polymethoxyflavones (PMFs) are citrus-specific flavonoids with important nutritional benefits; however, their transcriptional responses to heat stress remain poorly understood. Here, five-month-old ‘Ponkan’ citrus seedlings were exposed to 40 °C for 6, 11, and 21 days. HPLC analysis showed that the accumulation of four major PMFs (sinensetin, nobiletin, tangeretin, and 5-demethylnobiletin) was significantly reduced in leaves under heat stress. RNA-seq identified 3424 differentially expressed genes shared across all three time points, which were enriched in pathways associated with microtubule cytoskeleton organization, cell cycle regulation, and glyoxylate and dicarboxylate metabolism. Further analysis of the PMF biosynthetic pathway revealed that 14 of 18 key structural genes, including CHS, CHI, FNSII, and OMT family members, were downregulated by heat treatment. In addition, several bHLH, AP2/EREBP, and MYB transcription factors, known regulators of flavonoid biosynthesis, exhibited expression patterns closely associated with PMF accumulation. RT-qPCR analysis validated the transcriptome results. Collectively, these findings suggest that heat stress suppresses PMF accumulation through coordinated repression of PMF biosynthetic genes and their potential regulators. This study provides new insights into the molecular basis of heat-responsive PMF metabolism and offers potential targets for maintaining citrus nutritional quality under elevated temperatures.

Glutathione and Jasmonic Acid Biosynthesis Coordinate Antioxidant and Hormonal Responses to Alleviate Lead Toxicity in Pogonatherum crinitum Roots

The integrated regulatory network uncovered in this study provides promising candidate targets for breeding Pb-tolerant hyperaccumulators to remediate Pb-contaminated farmland and mining soil.

Progressive salinity drives flavonoid branch reprogramming in Anoectochilus roxburghii

Flavonoids play critical roles in plant adaptation to abiotic stress; however, how salt stress modulates metabolic flux distribution within flavonoid branches remains poorly understood, particularly in non-model medicinal plants. Here, we integrated targeted metabolomics, transcriptomics, and proteomics to examine flavonoid regulation in Anoectochilus roxburghii under 0, 50, 100, and 200 mmol·L− 1 NaCl. Metabolite profiling showed that salinity reshaped flavonoid composition rather than uniformly increasing flavonoid abundance. A metabolite-derived branch bias index (MI), representing the balance between reductive branch metabolites and flavonol products, increased under salt treatment, peaked at 100 mmol·L− 1 NaCl, and declined at 200 mmol·L− 1, indicating maximal branch bias under moderate stress followed by partial rebalancing under severe stress. Transcriptomic analysis showed induction of upstream phenylpropanoid and flavonoid entry genes, including PAL, 4CL, and CHS, whereas F3H was suppressed and FLS showed no induction. Furthermore, several short-chain dehydrogenase/reductase homologs (IFR-like SDR homologs) were upregulated, and the transcript-derived reductive branch index (EI) increased progressively across the salt gradient. EI was positively associated with MI, although the relationship was not strictly proportional under severe stress (200 mmol·L− 1 NaCl). Proteomic profiling further provided supportive evidence for sustained activation of upstream flavonoid biosynthesis, such as salt-induced accumulation of chalcone synthase (CHS) protein, complementing the transcriptomic and metabolomic datasets. Together, these results indicate that salt stress reorganizes flavonoid metabolism in A. roxburghii through persistent upstream activation and branch-specific regulation, favoring the reductive branch under moderate salinity. Salt stress reprograms flavonoid branch reprogramming in Anoectochilus roxburghii, coupling sustained upstream activation with repression of the flavonol node and preferential engagement of the reductive branch.