Fig. 1

The octoploid “EA78” genome assembly and the turnover of centromeric satellites. A Plant materials and experimental design. The parental cultivars are both octoploids with four subgenomes (A, B, C, D), following the subgenome designation of Jin et al. (2023) [14]. Pat: paternal, Mat: maternal. B A two-step phased assembly strategy for achieving global phasing by integrating HiFi, Hi-C, ONT Ultra-long sequencing data, and pedigree information. Note: UL: ultra-long. PSK: paternal-specific k-mers. MSK: maternal-specific k-mers. HER: hamming error rate. C Construction of a nearly complete and fully phased assembly of the “EA78” genome. The genomic locations of putative centromeres were shown in each chromosome. Arrows highlighting six chromosomes lacking canonical centromeric repeats. D The characterization of canonical centromeric repeats. Left: sequence similarity (based on average nucleotide identity, ANI) among centromere repeats of F. vesca, paternal and maternal assemblies, and sequence for fluorescent prove design. Middle: “EA78” chromatin number statistics. Right: FISH assay using the type I centromeric satellites as probes (scale bar = 5 μm)