Unveiling transcriptional regulation underpinning chilling and frost stress response in Trans-Himalayan Hippophae tibetana L.

Hippophae tibetana is an enigmatic least explored Seabuckthorn species, with exceptional adaptability to sub-zero temperatures in Trans-Himalayan region. This study integrates physiological and transcriptional profiling to understand its unique cold stress resilience. The physiological assessment including chlorophyll content, relative water content, and electrolyte leakage were least affected during the early response (ER) of cold stress as compared to prolonged (PR) and freeze response (FR), which was effectively restored during the recovery phase (RR). Genome-guided de novo assembly yielded 25,176 high-quality unigenes (N50: 2195 bp; BUSCO: 92.9%), with 75.9% functionally annotated using NCBI-nr, Araport11, SwissProt, COG, KEGG, and Pfam databases. Clustering of differentially expressed unigenes revealed ER (4467 DEGs) and RR (4478) grouped distinctly from PR (14,150) and FR (14,528), underscoring significantly heightened transcriptional reprogramming during PR/FR compared to ER/RR. Furthermore, the integration of transcriptional interactome network with GO and KEGG enrichment highlighted ICE1-CBF regulatory network with significant upregulation of Inducer of CBF Expression (ICE1), Cold receptive protein kinase (CRPK1), anti-freeze proteins (AFPs), and pathways like jasmonic acid signaling, carbohydrate metabolism, and membrane stabilization as key to cold tolerance during PR and FR phases. The current study advances our understanding of cold stress resilience in H. tibetana, elucidating its adaptive mechanisms in extreme Trans-Himalayan environments. The comprehensive genomic resources and key candidates identified here may provide a foundation for discovering cold tolerance-associated genome-wide variations in priority crops and plantation species.