Fig. 4: Comparative 3D genome architecture between 0B and 1B A. latifasciata genomes.

a Boxplot comparison of short-range versus long-range chromatin contact frequencies in 0B and 1B genomes. b Hi-C contact decay curve showing contact frequency as a function of genomic distance at 50 kb resolution. The 0B genome (blue line) is enriched for short-range contacts (<1 Mb), while the 1B genome (red line) displays more long-range interactions (>1 Mb). c Correlation between the number of TADs (y-axis) and chromosome size (x-axis) in both 0B and 1B genomes. The 1B genome features longer but fewer TADs compared to the 0B genome. d Distribution of TAD sizes in 0B and 1B genomes. e Number of duplicated regions predicted by SyRI between the two genome types, and f correlation between TAD size (x-axis) and the number of duplications (y-axis). Each point represents a TAD, colored by genome (blue = 0B, red = 1B) and scaled by TAD size. g High-resolution in situ Hi-C heatmaps of LG8 (25 Mb region) for 0B (top panel) and 1B (bottom panel) genomes at 50 kb resolution. TADs appear as “mountains,” with fewer, larger TADs in 1B. TAD separation scores (see Methods) are shown as tracks, with vertical lines indicating boundary positions. h Comparative Hi-C contact maps at 40 kb resolution showing loop structures (red dots) in 0B and 1B genomes. i Bar chart summarizing the total number of TADs and chromatin loops identified in each genome.