Lizuiyue Li, Nannan Zhang, Liqiang Hou, Xiaozhu Guo, Huizhe Feng, Yongzhi Yang, Bin Tian
•Chromosome-scale genomes of two Eremogone species.•A recent shared genome triplication shaped Caryophyllaceae evolution.•Reconstruction of the ancestral Caryophyllaceae karyotype (ACK, n = 9).•Biased gene retention after triplication is linked to alpine adaptation.•Multi-tissue transcriptomes link regulatory divergence to alpine adaptation.