Comparative population genomics reveals convergent and divergent selection in the apricot–peach–plum–mei complex

Abstract

The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits, however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aim to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the Apricot-Peach-Plum-Mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes with 251.25 Mb and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of approximately 1.17 Mb in the apricot genomes compared to peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stresses, flower development, and fruit ripening, along with divergent selection shaping crop-specific genes, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal co-linearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.