Fig. 2

Phylogenomic comparisons of centromeric repeat among wild and cultivated strawberries. A Investigation and production of a specific antibody for CEHN3 in octoploid strawberries. Eight CENH3 homologs were identified in octoploids using the F. vesca CENH3 protein sequence (LOC101294590). Eight CENH3 homologs were compared to determine the optimal polypeptide region for antibody production. B Multiple lines of evidence support the ability of the strawberry specific CENH3 antibody to recognize centromere regions. Using paternal chromosome 1A as an example, from top to bottom: CENH3 enrichment [log2(ChIP/Input); bin size: 1000 bp] using a common antibody (the light blue for original data, dark blue for smoothed data); CENH3 enrichment [log2(ChIP/Input); bin size: 1000 bp] using CENH3-specific antibody (light red for original data, dark red for smoothed data); distribution of type I centromeric satellite repeats on chromosomes (bin size: 1000 bp); distribution of Hi-C interaction signals (high interaction densities of interactions in red, low densities in white). C Sequence similarity matrix for 10 representative centromeres (including six neocentromere). D Identification and clustering of centromeric satellites. Letters A, B, C, and D represent subgenomes A, B, C, and D, respectively. Letters P and M represent paternal and maternal assemblies. E Average nucleotide identity (ANI) among four centromeric satellite types. Gray blocks indicate ANI values below 80. F ANI similarity matrix for centromere regions of homologous and homoeologous chromosomes. G Structural feature of the centromere region of Chr 5. The heatmap shows a high-resolution sequence similarity matrix of centromere regions (bin size: 2000 bp). H Identification and distribution of centromeric satellite repeats for each chromosome in F. vesca (FVES), F. chiloensis (FCHIL), F. virginiana (FVIRG), and “EA78” (EA). Different colors represent centromeric satellite types: red (type I), purple (type II), orange (type III), blue (type IV-1), and light blue (type IV-2). I FISH assay of F. chiloensis and F. virginiana using type I centromeric repeats as probes (scale bar = 5 μm). J Centromeric satellite similarity among F. chiloensis (Fchil), F. virginiana (Fvirg), and “EA78” (EA). Letters A, B, C, and D represent subgenome A, B, C, and D, respectively. Letters p and m represent paternal and maternal assembly, respectively. Numbers 1 and 2 represent haplotypes 1 and 2, respectively. K Ternary diagram showing the relative proportions of centromeric satellites of corresponding chromosomes in the three species. Haplotype 1 corresponds to the paternal assembly, haplotype 2 corresponds to the maternal assembly. Colors represent subgenomes: red (A), blue (B), orange (C), and cyan (D). Dot size represents the number of centromeric satellites. L Comparison of centromeric satellite numbers in the A subgenome of three octoploid species, with each data point representing one chromosome. F. vesca has only one consensus assembly (n = 7), while F. chiloensis, F. virginiana and “EA78” have both haplotypes (n = 14)