Fig. 1

Paired structure of the D. coronatus genome. a Dot plot of all-vs.-all comparison of the scaffold sequences. Alignments with 90% or more identity are plotted. For most sequences, purple line fragments are found indicating the presence of partner sequences with about 94% identity. Both axes are ordered to emphasize paired structure of the genome by MUMmer. Along the X-axis the scaffolds that have homologous counterparts are ordered by length (longest first), and along the Y-axis the corresponding counterpart scaffolds are arranged. Red lines indicate trivial hits to themselves. b A long syntenic region (1.3Mbp) is visualized using the GBrowse syntenic browser. 65% of the scaffold scf7180000986866 (lower box) and its homologous region in the scaffold scf7180000986886 (upper box) are shown. The thick green bars indicate sequences that have homologous counterparts; these are linked by light green shading. A few unpaired short bars indicate that their counterparts are found in other parts of the genome, probably as a result of translocation. Scale unit is Mbp. c For a detailed view of the paired structure, a 20 kbp region is magnified. Gene models (yellow or pink, boxes show exons and arrows show the gene orientation) and the histograms of RNA-seq coverage are shown under the gene models in both boxes. In the lower box, numbers of mismatches per 100 bp window (cyan) and lengths of insertions and deletions (blue and red, respectively, shown at 1 bp before In/Del site) are plotted in the 3rd and bottom rows, respectively. Scale unit is kbp