Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [HiC]

We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism. This series includes data for Hi-C for D. melanogaster, D. busckii, and D. virilis and genome assembly for D. busckii and D. virilis. Genome assembly data are available at the foot of this record. Previously published whole genome sequencing data were used in the assembly of the D. busckii contigs. Re-analyzed data includes PRJNA274996 (SRR1795010, SRR1794619, SRR1794616, SRR1794617, SRR1794614) and PRJNA196337 (SRR826809).