Comparative genomics clarifies phylogenetic relationships and genome evolution in Hippophae from the Qinghai-Tibet plateau.

The uplift of the Qinghai-Tibet Plateau (QTP) and associated climatic oscillations have shaped plant evolution, yet how adaptive strategies diversify along elevational, moisture, and latitudinal gradients within a single clade remains poorly understood. Hippophae (Elaeagnaceae) is distributed along these gradients, with all members sharing Frankia-mediated nitrogen-fixing symbiosis and dioecy. Here, we assembled chromosome-level genomes of H. neurocarpa, H. rhamnoides subsp. yunnanensis, and H. rhamnoides subsp. turkestanica, integrated them with four published assemblies, covering seven taxa (species and subspecies) of the genus. Whole-genome phylogenies dated the major intra-generic divergences to 6.71-2.83 Ma, coinciding with QTP uplift and Asian monsoon intensification during the late Miocene-Pliocene. Two ancient whole-genome duplications (ca. 35-40 and 25-30 Ma) predated the radiation, with retained paralogs significantly enriched in plant hormone signaling, ABA/MAPK cascades, cold-stress response, and reactive oxygen species metabolism. LTR retrotransposons showed a cross-species insertion peak at ∼ 0.2 Ma, and their flanking genes were repeatedly associated with ABA signaling, cold and UV-B responses, and flavonoid metabolism, suggesting a possible link to Pleistocene oscillations. Pan-genome analysis revealed core gene families comprising ∼ 55% of the pan-genome, while variable families differed along ecological gradients, with high-elevation H. tibetana harboring the highest proportion of species-specific genes. Lineage-specific positively selected genes were enriched in DNA damage repair, translational fidelity, and stress signaling. Together, these findings suggest that multidirectional ecological divergence in Hippophae was associated with ancient duplicate retention, transposon-associated regulatory variation, and lineage-specific selection, exemplifying rapid adaptive diversification in plants of the QTP and adjacent regions.