Genomic evidence for evolutionary history and local adaptation of two endemic apricots (Prunus hongpingensis and P. zhengheensis) with small populations

Endemic species usually have limited distribution ranges and are more vulnerable to extinction due to the global warming and anthropic activities. Here, two endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH), are focused on in this study to characterize their phylogenetic relationship, genetic diversity, demographic history, interspecific gene flow and genomic basis of local climate adaptation using whole-genome resequencing data. Our results suggest that PHP and PZH clustered into a lineage which shows a closer relationship with P. armeniaca compared to P. mume, and the estimated divergence time between these two species is ~ 0.94 Mya. The continuously decreased effective population size after the Large Glacial Maximum (LGM) have been observed in these two endemic apricots and possibly causes the current small populations of them. Despite the decreasing genetic diversity and heterozygosity are observed, we do not find the accumulation of deleterious mutations in these two endemic apricots, probably, due to the low inbreeding coefficient and strong purifying selection. Moreover, we have identified a set of positively selected genes during the local environmental adaptation of them that are important for the future molecular breeding of other cultivated apricots. Taken together, this study not only provides insights into the evolutionary history of two endemic apricots from a genetic perspective, but also has important implications for the conservation and future molecular breeding under the rapid future climate change.