Fig. 3: Analysis of flowering regulation of the genus Prunus.

a Record of flowering times across different Cerasus plants. The top image shows the onset of bud swelling, the middle image corresponds to the green tip stage, and the bottom image represents the full bloom stage. b Phylogenetic relationships among cherry species. Bootstrap support values are indicated by colored dots on major nodes, with red dots (BS > 90) and green dots (50 < BS ≤ 90). Prunus cerasus is an allotetraploid species derived from the natural hybridization of P. avium and P. fruticosa. The haplotype-resolved assemblies, P. cerasus (hapF) and P. cerasus (hapA), correspond to the subgenomes originating from P. fruticosa and P. avium, respectively. c Presence and absence of genes associated with flower development across different cherry genomes. Flower buds or flower samples from P. pseudocerasus, P. mahaleb, and P. avium were collected at three time points during the 2024 growing season: February 20 (T1), March 10 (T2), and March 25 (T3). d Highly relevant module (correlation ≥ 0.9) with flower development among three species. The gray square contains the gene number of the module (purple) and the subset annotated as floral development–related genes (blue). e Overlap of homologous genes of A. thaliana within the correlation module is shown as a Venn diagram, together with the number of candidate target genes in Pavi-T, Ppse, and Pmah (Bar chart). f Expression trends of the representative target gene across the three sampling time points (T1, T2, and T3).