Laidlaw, R.; Sanchez, M. G.; Pacheco, J. D. S.; Paradela, L. D. S.; Otto, T. D.; De Rycker, M.

Trypanosoma cruzi, the causative agent of Chagas disease, exhibits a complex life cycle with multiple hosts, stages and differentiation steps, all associated with extensive transcriptomic changes. Here we present a cell atlas for the T. cruzi life cycle, based on single cell transcriptomes for over 31,000 cells. We validated the atlas using known life cycle stage markers and population-based transcriptomics and show that the atlas can be utilised to accurately annotate life cycle stages in novel data. The atlas reveals many life cycle stage-associated genes and key transcriptomic differences between two amastigote-derived trypomastigote subtypes. Finally, enabled by single-cell resolution, we define the transcriptomic changes that occur across the epimastigote to metacyclic trypomastigote differentiation axis. This atlas provides not only a comprehensive resource for the study of T. cruzi biology, but also an unprecedented look at the complex changes that occur across the parasite life cycle.