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.FindingsHere, 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.ConclusionsWe 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.
Highlights
Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide
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
The coverage of individual Shae.V2 genome scaffolds was assessed by mapping short-insert, mate-pair (800 bp and 2, 5, and 10 kb), Chicago long-range, and Pacific Biosciences (PacBio) reads to the assembled scaffolds using Semi-HMM-based Nucleic Acid Parser (SNAP)-align or basic local alignment with successive refinement (BLASR) [49]
Summary
Human schistosomiasis is a chronic, neglected tropical disease affecting >200 million people worldwide and resulting in >300,000 deaths each year [1]. The coverage of individual Shae.V2 genome scaffolds was assessed by mapping short-insert (insert size: 170 and 500 bp), mate-pair (800 bp and 2, 5, and 10 kb), Chicago long-range, and PacBio reads to the assembled scaffolds using SNAP-align (for Illumina reads) or BLASR (for PacBio reads; v.2.2.0.133377, RRID:SCR 000764) [49]. Following filtering, published Illumina mate-pair and short reads (BioProject: PRJNA78265) [14], corrected PacBio reads, and Chicago reads were used to rescaffold and assemble Shae.V1 contigs into the refined Shae.V2 genome for S. haematobium (Table 1). The latter genome was assembled into 666 scaffolds (previously 99,953). The 5 representatives of the latter group included here were very closely interrelated, consistent with previous phylogenetic analyses and with the ability of some species to cross-hybridize [73, 86]
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