Whole-genome comparison of <i>S</i>. <i>bovis</i> and <i>S</i>. <i>haematobium</i>.

<p>A) Whole-genome comparison of <i>S</i>. <i>bovis</i> and <i>S</i>. <i>haematobium</i> (Egypt isolate) reveals remarkably high sequence similarity and provides evidence of interspecific hybridization. Pairwise alignments were carried out using mafft and the sequence identity calculated for 1 kb windows across the resulting alignments. Chromosome numbers were assigned by mapping <i>S</i>. <i>bovis</i> scaffolds to the <i>S</i>. <i>mansoni</i> genome assembly (autosomal chromosomes 1–7 and sex chromosome W). Regions with very high sequence similarity (sequence identity >99%) provide evidence of recent interspecific hybridization and are marked by blue arrows. Red lines depict segments with similar similarity levels, which were found by fitting a piecewise constant curve using a least-squares cost function. Grey shaded regions indicate mauve alignment blocks. The top coloured bar represents the <i>S</i>. <i>bovis</i> scaffold of each 1kb window and gaps represent regions of the <i>S</i>. <i>bovis</i> genome that were not aligned to the <i>S</i>. <i>haematobium</i> genome using mafft. B) Two remarkably similar regions on chromosome 4. Arrows mark breakpoints between highly similar and less-similar genomic regions. Top coloured bar represents <i>S</i>. <i>bovis</i> scaffolds and orientation (+/-). Repetitive elements (LINEs, LTRs, SINEs and others) are shown as coloured bars. The regions span protein-coding genes, intergenic regions and repetitive elements. High sequence similarity of repeats is indicative of recent <i>S</i>. <i>bovis-haematobium</i> hybridization, as the lower selective pressure acting on repetitive elements would otherwise lead to a rapid accumulation of mutations.</p>