Fig. 1

Overview of assembly quality, Muller placement, size, and annotation of genes, TEs, and satellites. A Phylogenetic tree produced by OrthoFinder based on the consensus of all gene trees. Species subgroups are numbered 1–6. Tree scale shows (0.05) rate of substitutions per amino acid site. B N50 values of unscaffolded assemblies published by Kim et al. [28] (gray) and assemblies scaffolded in this study (blue) in Mb (million base pairs). The dashed line indicates the minimal N50 value after scaffolding (D. mauritiana) among all 30 species. C Percentage of genomic sequence placed within Muller element scaffolds (green) or unplaced scaffolds (orange). D Size of scaffolded genome assemblies in Mb. Non-repetitive DNA shown in dark shade, repetitive DNA shown in light blue. E Number of thousands of genes with (dark) and without (light) identified D. melanogaster orthologs. The dashed lines indicate the minimal and maximal non-repetitive genome sizes. F Share of annotated transposable elements (TE) classes as percentage of genomic sequence. G Share of satellite DNA as percentage of genomic sequence that are located within Muller element scaffolds (green) or unplaced scaffolds (beige)