Figure 4.

The X chromosomal analyses for disease genes. (A) Numbers of female-specific (left) and male-specific reproductive disease genes (right) are plotted against all protein-coding genes with gene ages on chromosomes. The linear formulas fitted for autosomal genes at ancient (Euteleostomi) and younger (post-Euteleostomi) stages are shown in red and blue, respectively. The X chromosome is shown with triangles. (B) The ratios of male to female reproductive disease gene numbers (α) across four phylostrata. (C) The comparison of selection pressure (human-chimpanzee pairwise Ka/Ks ratios) for sex-specific reproductive disease genes between the ancient (Euteleostomi or older) and younger (post-Euteleostomi) phylostrata. Only the autosomal comparison is shown, with p value from the Wilcoxon test. (D) The numbers of male-specific reproductive disease genes (m) and the background genes (b) within the subregions from old to young in the X chromosome are provided, with the numbers displayed within round brackets for each subregion (m/b). SM, SCM, and HOS denote three classification methods for X chromosome structure: the substitutions method (SM) (Lahn and Page 1999; McLysaght 2008), the segmentation and clustering method (SCM) (Pandey et al. 2013), and the synteny method (orthologous gene order conservation between human and opossum, HOS) (Ross et al. 2005). (E) The fraction of disease genes with male-specific reproductive disease phenotypes within each X chromosomal subregion, as illustrated in (D), is presented. The gene coordinates have been updated based on the hg38 reference with liftover. “A”, “X”, and “Y” indicate autosomes, X and Y chromosomes, respectively.