Assessment of neo-sex chromosome architecture
We previously identified six large scaffolds in the draft male assembly with low nucleotide variation that we predicted constituted the ancestral-X portion of the neo-X chromosome (Keeling et al., 2013c). In the new assemblies, these scaffolds were found at the terminal end of the neo-X scaffold in the same orientation and almost the same order as previously predicted, starting at approximately 58.3 Mb and 51.1 Mb for the male and female neo-X scaffolds, respectively (Supp. Fig. 6).
We also used BLASTn to determine where 800 putative neo-Y scaffolds from the draft assembly found by Dowle et al. (2017) were located in the new male assembly. Of these draft scaffolds, 454 matched to the male neo-X chromosome, and the remaining 346 draft scaffolds corresponded to 202 other scaffolds in the final genome (Supp. Tab. 9). The male neo-X chromosome spans 70 670 744 bp in length, and the 454 draft scaffolds corresponding to the neo-X chromosome were located between base pairs 1 440 820 and 59 293 732 (Supp. Tab. 10). These draft scaffolds were not contiguous but were instead interspersed along this region of the neo-X chromosome (Fig. 5). The remaining portion of the final neo-X chromosome downstream of base pair 59 293 732 lacked any putative neo-Y scaffolds and also broadly overlapped with the region of elevatedFST and Tajima’s D on the final female neo-X chromosome, described above. All these data consistently support the same location of the ancestral-X at the terminal end of the neo-X chromosome.