Fig. 2: Pangenome characteristics of the cherry.

a Number of pangenes and core gene families across different combinations of Cerasus genomes. The number of pan gene families and core gene families was independently stated 18 times when using a single genome and stated 21 times when using more than one genome. Each box represents the median and interquartile range (IQR), with whiskers extending to the maximum and minimum values. b Composition of the pangenome and individual genomes. The histogram displays the number of gene families across varying genomes, while the pie chart illustrates the proportion of gene families in each category. Gene families are classified as core (present in all genomes), softcore (over 90% of all genomes), private (over 90% of two genomes), and dispensable (the remaining) gene families. Orphan genes (that is, species-specific gene families with only one gene) were excluded. c Proportion of core, softcore, dispensable, and private genes within the Cerasus pangenome. d Structural variation (SV) density across each chromosome. e Proportions of SV types in the Cerasus pangenome, including deletion (DEL), duplication (DUP), insertion (INS), inversion (INV), and translocation (TRA). f Distribution of genomic characteristic elements across each chromosome. The circle layers from outermost to innermost represent: chromosome length, deletion density, insertion density, transposon elements, LTR density, GC content, and gene density. Species abbreviations: P. tianshanica (Ptia), P. subhirtella (Psub), P. speciosa (Pspe), P. spachiana “Komatsu-otome” (Pspa), P. serrulata (Psert), P. serrula (Psera), P. campanulata-F (Pcam-F), P. avium “Regina” (Pavi-R), P. pusilliflora (Ppus), P. pseudocerasus (Ppse), P. mahaleb (Pmah), P. incisa “Oshidori“ (Pinc), P. humilis (Phum), P. fruticosa (Pfru), P. conradinae (Pcon), P. cerasus (Pceru), P. cerasoides (Pcero), P. campanulata (Pcam), P. avium “Burlat” (Pavi-B), P. avium “13-33” (Pavi-13), and P. avium “Tieton” (Pavi-T).