High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the Drosophila virilis sub-group.

sub-group is an emerging model with an enticing combination of attributes, including abundant and diverse repetitive DNA content, structural rearrangements, and hybridization capability. The lack of high-quality genome assemblies for this group have prevented detailed understanding of genome evolution. Here, we present five new long-read genome assemblies of three virilis sub-group species along with analyses of structural variants, polymorphisms, repetitive DNAs, and Y chromosome genes and repeats. We find that the expansion and mobilization of non-canonical repetitive elements accounts for most of the divergence in assembled genome sequence between these species, with an especially striking takeover of the Y chromosome by a single type of element in one of the three species. Overall, our study positions the virilis sub-group as a model for a variety of future studies.