Whole-genome comparison of S. bovis and S. haematobium.

A) Whole-genome comparison of S. bovis and S. haematobium (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 S. bovis scaffolds to the S. mansoni 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 S. bovis scaffold of each 1kb window and gaps represent regions of the S. bovis genome that were not aligned to the S. haematobium 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 S. bovis 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 S. bovis-haematobium hybridization, as the lower selective pressure acting on repetitive elements would otherwise lead to a rapid accumulation of mutations.