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Fig. 3 | Genome Biology

Fig. 3

From: Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

Fig. 3

Identification of the sex-linked region. a p values (log10 transformed) of genome-wide association study for the sex trait (male or female). Re-sequencing data of ten male and ten female individuals were used. b The Y axis shows the density of male-specific SNPs (number per 50 kb window). Those SNPs are present in all ten males but not in females. c The zoom-in view of b on the Y chromosome. The male-specific SNPs are enriched in a ~7 Mb region. d The sequence similarity between the introns of the X and Y chromosomes. The similarity was calculated in every 100 kb window (black dot). Gene deserts were frequently seen in the R2 of the SLR. e The R1 region tend to have a higher density male-specific SNP and has a significantly lower X-Y sequence similarity than the S2 region (Wilcoxon sum rank test). f Sequence synteny between the X and Y chromosome. No large-scale inversions were observed. The SLR (R1 and R2) are highlighted by color. g, h Similar chromosomal compartmentalization between the X and Y chromosome. In the top panel, the colors of dots measure the frequency of chromatin interacting between 100 kb windows. Interactions across the centromere are infrequent. The first panel in the lower part shows the proportions of repeats of every 50 kb sequence (a dot) and highlighted in dark purple when it is larger than 40%, otherwise in orange. The second panel shows the proportions of the Cen-524 satellite in 100 kb windows. The third panel shows the gene density measured as the number of genes in 100 kb windows. The Y-axis of the H3K9me3 panel shows the −log 10 transformed p values for the H3K9me3 peak calling. The PC1 panel shows the PC1 values of Hi-C epivector: the positive values (red) represent active A compartments and the negative values (blue) represent silenced B compartments. The locations of centromeres were denoted by a dashed vertical line

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