Assessment of neo-sex chromosome architecture
Identification of the neo-Y and ancestral-X portions of the neo-sex chromosomes may clarify the process of sex chromosome evolution in mountain pine beetle. Previous work has identified likely neo-Y scaffolds (Bracewell et al., 2017; Dowle et al., 2017) and ancestral-X scaffolds (Keeling et al., 2013c) in the draft male genome assembly. We assessed the genomic locations of the putative neo-Y scaffolds in the final male genome assembly with BLASTn as described above, using the final male assembly to create a custom database and then blasting the draft scaffolds identified by Dowle et al. (2017) against it. We also used NUCmer to identify the regions of the neo-X chromosome derived from the ancestral-X scaffolds of the draft male assembly predicted by Keeling et al. (2013c).