Fig. 3: Comparative ATAC-seq in the genus Schmidtea to assess regulatory element conservation.

a Evolutionary distance of the analyzed Schmidtea species on the basis of 4-fold degenerate sites in the whole genome alignments. Branch lengths indicate expected substitutions per site. The tree topology is based on a phylogenomic analyses of 930 single-copy genes and agrees with previous work⁵⁹. b Hi-C contact maps of the genome assemblies of S. polychroa (schPol2), S. nova (schNov1), and S. lugubris (schLug1). c BUSCO completeness assessment of the genome assemblies (left three bars) and the corresponding annotations (right bars) of the new Schmidtea genomes. Since the annotation assessment was run on the transcript level, the “Duplicate” and “Complete” category were combined for the visualization to avoid apparent duplication due to isoforms. d ATAC-seq fragment-size distributions of the indicated species. e Pileups of nucleosome-free region (NFR) and mononucleosomal (mono) reads at transcription start sites (TSS) of the indicated species. f Schematic diagram showing the definition of a conserved region (sequence conservation without ATAC-seq signal) and conserved peak (sequence conservation and ATAC-seq signal). g Bar plots indicate the conservation status of all S. mediterranea ATAC-seq peaks by conservation category and the degree of conservation across the sister species. The “conserved” bar sub-categorizes the 13.6% of highly conserved peaks according to the histone mark categorization in Fig. 2i. The three bar plots represent the conservation status of putative promoters, putative enhancers, and uncharacterized ATAC-seq peaks. h Highly conserved regulatory elements in association with the wnt1 gene locus. Top: Representation of the S.mediterranea gene locus, including sequence conservation (PhyloP on whole genome alignments), H3K4me3 ChIP, H3K27ac ChIP, and ATAC-seq tracks, annotated regulatory elements (published³⁹, black; this study, blue), and the exon/intron representation of the wnt1 gene. Below, the available tracks in the three sister species genomes are shown aligned by the TSS. Note, that only a single peak was called in S. nova and the peak was therefore classified as a conserved region in that species. Source data are provided as a Source Data file.