Pangenome and resequencing analyses reveal flowering evolution and genetic control in Cerasus

Prunus subgenus Cerasus contains numerous species with ornamental, edible, and medicinal value. However, limited genomic resources have constrained systematic analyses of structural variation and the genetic basis of key phenological traits in this group. Here, we assemble eight genomes from diverse Cerasus species. Together with 13 published genomes, we construct a pangenome of 21 accessions representing 17 species. Phenological observations reveal substantial variation in flowering time. Integrating comparative genomics, transcriptomics, and population genetic analyses highlight candidate regulators of flowering time. We find that AGAMOUS-LIKE 9 (AGL9) is strongly associated with flowering progression. Both ectopic expression and transient overexpression of PavAGL9 can accelerate post-dormancy flowering progression. We reveal that PavBPC6 binds the PavAGL9 promoter and represses its transcription, indicating a negative regulatory role. Furthermore, PavAGL9 interacts physically with PavSEP1 and PavPMADS2, suggesting synergistic roles in floral organ development. Our pangenome resource establishes a comprehensive genomic framework for Cerasus and provides insights into the regulation of flowering progression.