Fig. 3

Potential regulatory regions and 3D structure of duck genome. A The ATAC-seq signal enrichment around the transcription start sites (TSSs) for two representative samples. B The number of narrow peaks detected in 12 samples and the narrow peaks detected by irreproducible discovery rate (IDR) was considered as confidence peaks (P < 0.01). The P0, P3, and P5 represent subcutaneous adipocytes that begin to differentiate and differentiate for 3 days and 5 days, respectively. The F0, F3, and F5 represent abdominal adipocytes that begin to differentiate and differentiate for 3 days and 5 days, respectively. C Length distribution of identified chromosomal accessibility regions. D The proportion and distance of chromatin accessibility regions annotated to the different structures of genes. The upper bar graph represents the proportion of chromatin accessibility regions annotated to the gene structure, such as promoter, exon, and UTR. The bar graph below shows the distance from the closest chromatin accessibility region to the gene TSS. E ATAC-seq and RNA-seq enrichment and correlation map of a Hi-C matrix for chromosome 7 at 100-kb resolution (res) in mallard breast muscle. The chromatin activity and expression level of the “A” compartment are higher than those of the “B” compartment. F Open chromatin and gene expression in the active “A” compartment (ATAC-seq n = 147,398; gene n = 8165) and the inactive “B” compartment (ATAC-seq n = 99,246; gene n = 3579). A two-sided unpaired Wilcoxon test was used to calculate P-values. G The TAD structures of chromosome 7 in mallard and Pekin ducks were detected at 50-kb resolution, among which mallard duck contained 48 TAD structures, and Pekin duck contained 43 TAD structures