Supplemental Material for Bracewell et al., 2020

Figure S1 shows an Integrative Genomics Viewer image of a region on Muller A of the genome assembly with mapped Hi-C reads filtered for Pilon polishing. Figure S2 contains a plot of Illumina and Nanopore sequencing coverage over the draft genome assembly. Figure S3 shows the Hi-C heatmap and scaffolding as in Figure 1 with nucleotide diversity (π) estimated from the isofemale line in 50kb non-overlapping windows across the assembly. Figure S4 displays the genomic distribution of the ten most frequently encountered transposable elements (TEs) for each Muller element in the genome assembly. Figure S5 shows the genomic location of D. subobscura pericentromeric orthologs from Muller C and D on the fused Muller CD of D. bifasciata.

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