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It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV\/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of<jats:italic>S<\/jats:italic>.<jats:italic>haematobium<\/jats:italic>is required. Hybridisation\/introgression events and molecular variation among members of the<jats:italic>S<\/jats:italic>.<jats:italic>haematobium<\/jats:italic>-group might effect important biological and\/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover \u2018new\u2019 genes and transcription profiles for these stages, likely linked to development and\/or pathogenesis. Molecular variation within<jats:italic>S<\/jats:italic>.<jats:italic>haematobium<\/jats:italic>among some geographical locations in Africa revealed unique genomic \u2018signatures\u2019 that matched species other than<jats:italic>S<\/jats:italic>.<jats:italic>haematobium<\/jats:italic>, indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of<jats:italic>S<\/jats:italic>.<jats:italic>haematobium<\/jats:italic>and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.<\/jats:p>","DOI":"10.1371\/journal.ppat.1010288","type":"journal-article","created":{"date-parts":[[2022,2,15]],"date-time":"2022-02-15T18:57:49Z","timestamp":1644951469000},"page":"e1010288","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":35,"title":["Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation"],"prefix":"10.1371","volume":"18","author":[{"given":"Andreas J.","family":"Stroehlein","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pasi K.","family":"Korhonen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V. 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