Over 250 million people suffer from schistosomiasis, a tropical disease caused by parasitic flatworms known as schistosomes. Humans become infected by free-swimming, water-borne larvae, which penetrate the skin. The earliest intra-mammalian stage, called the schistosomulum undergo a series of developmental transitions. These changes are critical for the parasite to adapt to its new environment as it navigates through host tissues to reach its niche, where it will grow to reproductive maturity. Unravelling the mechanisms that drive intra-mammalian development requires knowledge of the spatial organisation and transcriptional programs of the different cell types that comprise the schistomulum body. To fill these important knowledge gaps, we performed single-cell RNA sequencing on 2-day old schistosomula of Schistosoma mansoni. We identified gene expression programs representing muscles, nervous system, tegument, parenchymal cells, and stem cells. We validated cell markers for all these clusters by in situ hybridisation in schistosomula and adult parasites. Together, this study provides a comprehensive cell-type atlas for the early intra-mammalian stage of this important parasite. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
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