Fig 6. Genomic context of the Y-chromosomal region surrounding OGI.

a, Read coverage from male (blue) and female (pink) samples and male/female coverage ratio across the scaffolds covering the male-specific region of the Y-chromosome. For both the male and female reads, expected coverage a single-copy sites is approximately 20 (grey lines across). This male-specific region was assembled via anchoring of the scaffolds with BAC sequences. Approximately 1.3Mb region was covered by Y-allelic scaffolds. More than 400kb of long repetitive sequences (dotted lines), flank OGI. Outer regions of these hyper repetitive sequences contain male-specific sequences (blue bands in M/F rate) and pseudo autosomal region (PAR)-like sequences (orange lines), where M/F rate was less than 70%, and the percentage of repetitive sequences was much lower. b, The silent divergence rate (dS) between X and Y alleles of the genes located in the PAR-like sequences (orange circles) decreases with distance to OGI. Stil, for most of these genes, the dS value between the X and Y alleles was larger than the average interspecific dS between the X alleles of D. lotus and D. mespiliformis (green square and dotted line), D. lotus and D. virginiana (blue square and dotted line), and D. lotus and D. kaki (red square dotted line). These results suggest that, in these PAR-like sequences, recombination between the X and Y alleles was suppressed before the divergence of Diospyros species, or at least predates the divergence between D. lotus and D. kaki. dS values for genes located in the regions closest to OGI are comparable to dS values between OGI and MeGI (gray circle, dS = 0.205), which suggest that little or no recombination occurred between these sequences after the establishment of OGI. In comparison, dS values between the X and Y alleles of genes located in the recombining region of chromosomes 15 are much lower (while circles on the right).