Fig 1.
Comparison of the S. bovis proteome with other schistosome species.
A) S. bovis centred Venn diagram. The outer ring represents the 11,631 proteins predicted from the S. bovis genome, while the inner 3-way Venn diagram shows the subset of predicted S. bovis proteins that were present in the genomes of S. haematobium (Egypt isolate), S. mansoni and S. japonicum, respectively, based on protein sequence homology. The colours of the inner 3-way Venn diagram correspond to the number of proteins in each intersection from low (light grey) to high (dark blue). A Schistosoma core-proteome of 8,105 proteins was identified as those proteins that had sequence homology matches across all four species. 95 predicted proteins were unique for S. bovis. B) Sequence identity of S. bovis proteins and orthologous proteins from other schistosome species. Proteins of S. bovis and S. haematobium were significantly more conserved (p<10−15, two-tailed t-test) than the proteomes of S. bovis-S.-mansoni and S. bovis-S. japonicum. C) Sequence conservation of S. bovis tegument proteins and secreted peptides. S. bovis proteins were mapped to the S. haematobium genome sequence using Exonerate. Tegument proteins and secreted peptides showed an average sequence identity of 98.9% and 97.8%, respectively. All tegument proteins and secreted peptides included in this analysis were shared by both species. D) Analysis of the Schistosoma pan-genome. Proteomes of four Schistosoma species were concatenated, clustered into orthologous groups and mapped to each Schistosoma genome using Exonerate. Colours depict the number of proteins in each intersection from low (light orange) to high (dark orange). A pan-genome of 13,297 orthologous groups and a Schistosoma core-genome of 9,851 proteins were identified.
Table 1.
Characteristics of S. bovis, S. haematobium (Egypt isolate) [15], S. mansoni [13] and S. japonicum [16] genome assemblies.
Fig 2.
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.
Fig 3.
Phylogenetic tree and estimated divergence times.
A maximum-likelihood phylogenetic tree was inferred from concatenated protein sequences corresponding to 52 shared single-copy genes. Species divergence was estimated using a Bayesian relaxed molecular clock model. Divergence time is given in million years; 95% confidence intervals are shown in brackets. The divergence time between S. bovis and S. haematobium was estimated to be 1.85 million years (95% confidence interval 1.21–2.63 mya). The model was calibrated using previously published divergence times and ages of fossil records of intermediate snail hosts.