Figure 1.

Experimental flow chart. A heterozygous fly (H3) was produced by crossing ISO1 and I38 strains. A single female offspring was laterally dissected. From the posterior half, HMW DNA was extracted and used to prepare the two primary assemblies, a R2C2 genomic library for nanopore sequencing, and a Tn5 tagmentation library for paired end Illumina sequencing. The anterior portion was used to isolate intact chromatin to generate a Hi-C paired end Illumina library. The two primary assemblies were merged into one then arranged into chromosome length scaffolds using the Hi-C contact frequency data.