Genomic Insights into High-Altitude Adaptation: A Comparative Analysis of and in the Himalayas.

Environmental stress at high altitudes drives the development of distinct adaptive mechanisms in plants. However, studies exploring the genetic adaptive mechanisms of high-altitude plant species are scarce. In the present study, we explored the high-altitude adaptive mechanisms of plants in the Himalayas through whole-genome resequencing. We studied two widespread members of the Himalayan endemic alpine genus (Zingiberaceae): (a selfing species) and (an outcrossing species). These species are distributed widely in the Himalayas with distinct non-overlapping altitude distributions; is distributed at higher elevations, and occurs at lower elevations. Compared to , exhibited higher levels of linkage disequilibrium, Tajima's , and inbreeding coefficient, as well as lower recombination rates and genetic diversity. Approximately 96.3% of the genes in the reference genome underwent significant genetic divergence ( ≥ 0.25). We reported 58 completely divergent genes ( = 1), of which only 17 genes were annotated with specific functions. The functions of these genes were primarily related to adapting to the specific characteristics of high-altitude environments. Our findings provide novel insights into how evolutionary innovations promote the adaptation of mountain alpine species to high altitudes and harsh habitats.