A single-cell atlas of the miracidium larva of the human blood flukeSchistosoma mansoni: cell types, developmental pathways and tissue architecture

Schistosomes are parasitic flatworms that cause the water-borne disease schistosomiasis, affecting millions of people worldwide. The miracidium larva of schistosomes represents the first post-embryonic stage of development and is critical to transmission. After hatching, a miracidium infects a freshwater snail and transforms into a mother sporocyst, where its stem cells generate daughter sporocysts that give rise to many human-infective cercariae larvae. To understand this important life cycle stage at the cellular and molecular levels, we have used single-cell RNA sequencing,in situhybridisation and image analysis to create a whole-body cell atlas of the miracidium larva ofSchistosoma mansoni. Our atlas shows that each miracidium is composed of ∼365 cells and 19 transcriptionally distinct cell types. We show that 93% of miracidium cells are somatic (57% neural, 19% muscle, 13% epidermal (tegument), 2% parenchyma, 2% protonephridia), and the remaining 7% are stem cells. Cellular diversity within tissue types is revealed, and is highest in neurons. There are two stem cell populations, and they show different activation and potency states. Trajectory analysis indicates that one stem cell population is the origin of the tegument lineage and the other likely contains pluripotent cells. Furthermore, each of these stem populations is transcriptionally distinct based on sex-linked gene expression in male and female larvae. Through single cell transcriptomics andin-situhybridisation we identified every cell in the whole organism revealing the organisation of the miracidium. This single cell atlas provides the foundation to understand the development and interaction of cell types and tissues as they change over a life cycle that is characterised by complex morphological changes.