, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (, . ) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of is controversial. Thus, we generated a high-quality haplotype-resolved genome for . , exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of . , which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the gene in apricot and showed that the activity of the promoter increased under low temperatures. In addition, overexpression in indicated that positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of plants.