Stroehlein, Andreas J.Korhonen, Pasi K.Lee, V. VernRalph, Stuart A.Mentink-Kane, MargaretYou, HongMcManus, Donald P.Tchuenté, Louis-Albert TchuemStothard, J. RussellKaur, ParwinderDudchenko, OlgaAiden, Erez LiebermanYang, BichengYang, HuanmingEmery, Aidan M.Webster, Bonnie L.Brindley, Paul J.Rollinson, DavidChang, Bill C.H.Gasser, Robin B.Young, Neil D.2022-03-242022-03-242022Stroehlein, Andreas J., Korhonen, Pasi K., Lee, V. Vern, et al.. "Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation." <i>PLOS Pathogens,</i> 18, no. 2 (2022) Public Library of Science: https://doi.org/10.1371/journal.ppat.1010288.https://hdl.handle.net/1911/112051Urogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting > 100 million people. 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 S. haematobium is required. Hybridisation/introgression events and molecular variation among members of the S. haematobium-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 ‘new’ genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S. haematobium among some geographical locations in Africa revealed unique genomic ‘signatures’ that matched species other than S. haematobium, 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 S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.engThis is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.Journal articlejournal-ppat-1010288https://doi.org/10.1371/journal.ppat.1010288