Insect genomes vary extensively in size, chromatin structure, and chromosome number, but tend not to vary in gene number. Therefore, larger genomes tend to have more gene-poor heterochromatic regions. Previous work on cactophilic Drosophila in the nannoptera species group found that these specialist dipterans had highly heterochromatic chromosomes, suggesting they had large genomes. However, follow up work on genome size found that while these genomes are highly heterochromatic, they do not have a larger genome size than would be expected for most Drosophila species. Therefore, we are asking what types of rearrangements in the genome allow for such compaction and where do these heterochromatic sequences occur. In order to address this problem, we performed long-read sequencing with Oxford Nanopore Technology on males and females of D. acanthoptera and D. bromeliae, with subsequent Illumina sequencing. Drosophila acanthoptera is from the cactophilic nannoptera group, while D. bromeliae is sister to this group, and does not have a highly heterochromatic genome. As preliminary assemblies of D. acanthoptera have been found to be difficult due to repetitive heterochromatic content (genomes assembling smaller than estimated sizes), we assembled the genomes using multiple parameter configurations from three commonly used long-read genome assembly programs (Canu, Flye, and NextDenovo). We then performed BUSCO analysis to determine the completeness of these assemblies. Here we are presenting comparisons of the assembly statistics and BUSCO scores for male and female genomes for both species.