Fig. 1

General features of high-throughput chromatin conformation capture (Hi-C) heatmaps of the HD3 chicken cell line. a—Chromosome-scale view of the Hi-C heatmap of genomic contacts in HD3 (upper right) versus chicken embryonic fibroblasts (CEF) (lower left) with a normal genome. Karyotype abnormalities are identified as nondiagonal patterns of enriched interchromosomal interactions; b—Example of A/B compartment profile along GGA8 in HD3 cell line and CEF; c—Example of TAD profile and TAD coordinate calls (blue lines below) in 5 Mb region of GGA2 in HD3 cell line, CEF and chicken granulosa cells F1-1 from preovulatory follicles; d—Enlarged view of HD3 Hi-C heatmap square (a, blue), indicating abnormal enrichment of contacts in the terminal regions of GGA1 and GGA2 as well as significant loss of contacts near the centromere of GGA2. The interaction enrichment gradient is clearly seen along GGA2, starting from GGA2qter. The relative positions of breakpoint regions are shown as red lines on the schematic depictions of chromosomes