Fig. 5

Structural variations in the 3D genome. a Percentages of conservative and variable compartments with PAV, CNV, INV, and TRANS. P values were calculated by one-sided Fisher’s exact test. b Example of A/B compartments and structural variations. The pink colored lines represent large translocations between chromosome 11 and chromosome 13. c Percentages of structural variations around TAD boundaries. d Percentages of structural variations around common and specific TAD boundaries. e Percentages of structural variations around core, dispensable, and private TAD boundaries. f Snapshot of the structural variation catalog between the ZH13 genome and 26 query accessions. The brown box represents the 22.95–24.35 Mb region of Chr04 in ZH13. The color bars on the left represent five haplotypes in 27 accessions. The 26 collinear panels represent the collinearity and structural variations around the region, where the bottom line represents the ZH13 accession, and the top line represents the query accession in each panel. These query accessions from top to bottom are SoyL01, SoyL04, SoyC04, SoyC05, SoyC11, SoyC03, SoyC08, SoyL07, SoyC09, SoyC13, SoyC14, SoyL06, SoyC02, SoyC07, SoyC06, SoyW03, SoyL02, SoyL08, SoyC10, SoyC12, SoyW01, SoyW02, SoyL03, SoyL05, SoyL09, and SoyC01. g Examples of five haplotypes and Hi-C contact maps. The left panel represents the structural variations of the five haplotypes relative to ZH13, and the right panel represents the Hi-C contact maps of the five haplotypes in ZH13