Fig. 3

Characterization of genomic structural variations between the A. adenophora haplotypes. (a) Overview of syntenic blocks across the three haplotypes. Gray lines represent the syntenic regions, while orange lines represent the inversions. (b) Identification of large inversions in Chr14. The upper two heatmaps show a chromatin 300-kb interaction matrix, including mapping Hi-C data of A1_14 against the haplotype B genome (A1_map_B), mapping Hi-C data of B_14 against the haplotype A1 genome (B_map_A1). The middle panel shows the syntenic blocks across A1, B and A2 in chromosome 14. The largest inversion regions are shown by orange lines. The lower two heatmaps for A2_14 show a chromatin interaction heatmap with a similar mapping strategy as the upper track. (c) Consistent alignment of the BioNano contigs with the PacBio assembly demonstrates the inversion accuracy in the PacBio assembly. The red arrows indicate inversion breakpoints, while the black lines shown collinearity between the PacBio assembly and BioNano maps.