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. 2019 Sep 1;8(9):giz108.
doi: 10.1093/gigascience/giz108.

High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing

Andreas J Stroehlein  1 , Pasi K Korhonen  1 , Teik Min Chong  2 , Yan Lue Lim  2 , Kok Gan Chan  2 , Bonnie Webster  3 , David Rollinson  3 , Paul J Brindley  4 , Robin B Gasser  1 , Neil D Young  1
Affiliations

High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing

Andreas J Stroehlein et al. Gigascience. .

Abstract

Background: Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation.

Findings: Here, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available.

Conclusions: We report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions.

Keywords: Schistosoma haematobium; genome assembly; single-molecule and long-range sequencing.

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Figures

Figure 1:
Figure 1:
Comparison of schistosome genome assembly quality metrics. Scaffold lengths, N50, and L50 values for Schistosoma haematobium genome version 2 (Shae.V2), version 1 (Shae.V1), and S. mansoni are shown.
Figure 2:
Figure 2:
Comparison of the synteny and contiguity of assemblies for S. haematobium version 1 (Shae.V1) and version 2 (Shae.V2) genomes. Shae.V1 scaffolds (n = 810) are represented by orange bars and are linked with 135 Shae.V2 scaffolds (light blue bars). Scaffolds are arranged as a circular plot based on 5,506 regions containing single-copy orthologs (SCOs, each represented by a line connecting an orange with a blue scaffold). SCO lines have distinct colours for each Shae.V2 scaffold.
Figure 3:
Figure 3:
Comparison of the synteny, contiguity, and integrity of assemblies for S. haematobium version 2 (Shae.V2) and S. mansoni (WBPS8). Shae.V2 scaffolds (n = 79) are represented by orange bars and are linked with 8 S. mansoni chromosomes (light blue bars). Scaffolds are arranged in a circular plot based on 218 regions containing single-copy orthologs (SCOs, each represented by a line connecting an orange with a blue scaffold). SCO lines have distinct colours for each S. mansoni chromosome. Additionally, gaps (“Ns”) are represented as black histograms on a separate track, with the Y-axis representing the size of the region containing ambiguous nucleotides (range, 0–5,013). On the outer track, orange histograms represent areas of >1,000 bp in length for which the coverage of “properly paired” reads was <5 reads. Higher histograms represent longer regions. Dark green histograms within the same track represent regions of low “physical” coverage. The lower the histograms “drop” from the top of the track, the larger is the size of the regions that have “physical” coverage of <10 reads.
Figure 4:
Figure 4:
Assessment of genome completeness based on the identification of 978 curated, single-copy, metazoan genes in genomes (A, B) and gene sets (C, D) for schistosomes, using the program BUSCO. The proportion of BUSCO genes identified as complete (single or duplicated), fragmented, or missing (genome mode: A; gene set mode: C) and the number of predicted gene models homologous to complete BUSCO genes (genome mode: B; gene set mode: D) are shown for each genome.
Figure 5:
Figure 5:
Phylogenetic position of Schistosoma haematobium relative to other representatives of the class Trematoda, for which draft genomes were available. Trees constructed using Bayesian inference (BI, shown) and maximum likelihood (ML) analyses of amino acid sequence data inferred from 186 single-copy orthologs (SCOs) had the same topology. Nodal support values for BI and ML analyses are indicated at each branch (posterior probability/bootstrap support). Branch lengths represent the numbers of amino acid substitutions per site at aligned positions. Gyrodactylus salaris (class Monogenea) represents the outgroup. Inset image shows a pair of adult schistosomes.
Figure 6:
Figure 6:
Distribution of gene length for gene sets representing Schistosoma haematobium (Shae.V1 and Shae.V2) and S. mansoni (Sman.WBPS11). Additionally, distributions are shown for terminal genes (i.e., genes encoded at the start or end of a scaffold) for both S. haematobium gene sets (“Shae.V1 term.” and “Shae.V2 term.”). Statistically significant differences among distributions (independent 2-group Mann-Whitney U test) are indicated for P ≤ 0.001 (***).
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