Bioscience Evidence 2025, Vol.15, No.5, 209-218 http://bioscipublisher.com/index.php/be 212 epigenetics (Belteky et al., 2018). Furthermore, the foraging, breeding and social interaction patterns of domestic chickens have also changed due to artificial selection (Li et al., 2019; Mehlhorn and Caspers, 2021). Figure 1 A complete chicken genome with 10 dot chromosomes. (A) A trio-based genome assembly pipeline. Rounded rectangles represent contigs. Paternal and maternal contigs were used to fill gaps in the primary contigs. (B) The dot chromosomes are in general composed of a euchromatic part and a heterochromatic part. The asterisks denote newly assembled chromosome models. (C) A zoom-in view for chr29, showing CENP-A and H3K9me3 binding, coverage of Nanopore ultralong, HiFi, NGS (BGISEQ-500, dashed lines indicate genomic average), gene expression (RNA-seq read counts in 1 kb windows), 5-mC levels, and A/B compartments. (D) The heatmap shows the chromosomal sizes (log-transformed), GC content, repeat content, chromosome-wide 5-mC levels, and ChIP/input ratios for H3K9me3, H3K36me3, and H3K27me3. (E) Interchromosomal interaction frequency measured using Hi-C data. (F) Dot chromosomes have a lower Tau value, i.e., lower level of tissue specificity but a higher expression level. P values were calculated using the Wilcoxon signed-rank tests (Adopted from Huang et al., 2023) 4.4 Genetic underpinnings The domestication of domestic chickens has been accompanied by significant changes in the genome, including selection, mutation, deletion and the addition of exogenous genes. Genome-wide studies have found that domestic
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