Fig. 3.

Translocation of the shared male-specific region drove the turnover of sex chromosomes in Takifugu species. (A) The male-specific region in T. snyderi. We aligned resequencing reads from 24 males and 24 females against the assembled genome of a T. snyderi XY male and calculated the relative depth of coverage between sexes at a sliding-window size of 1 kb. In the upper plot showing the genome-wide analysis, scaffolds are on the x-axis. The lower plot shows the male-specific region on scaffold_373. The normalized coverage of males, females, and their ratio are shown in red, blue, and gray, respectively. (B) The male-specific region in T. vermicularis. We aligned resequencing reads from 7 males and 12 females against the assembled genome of a T. vermicularis XY male. In the upper plot showing the genome-wide analysis, contigs are on the x-axis. The lower plot shows the male-specific region found on contig utg000584l. Note that this contig contains large inverted duplications and a repeat-rich region (SI Appendix, Fig. S10B) in which paired-end reads cannot be mapped except in several segments. The contiguous sequence spanning all the male-specific segments was defined as the male-specific region. (C) Syntenic relationship between the male-specific genes of T. niphobles, T. snyderi, and T. vermicularis, and their homologs of T. rubripes. Each haplotype is annotated with pentagons to depict annotated full-length genes. Arrows indicate CACTA transposable elements containing the catalytic center of a transposase. (D) Maximum-likelihood clustering of the male-specific and autosomal paralogs in T. niphobles, T. snyderi, and T. vermicularis. Red and blue colors represent the male-specific (-Y) and autosomal (-A) paralogs, respectively. TN, T. niphobles; TR, T. rubripes; TS, T. snyderi; TV, T. vermicularis. The autosomal orthologs in Torquigener hypselogeneion (ToH) were used as outgroups. Bootstrap values are shown at the nodes of each tree.