A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression

Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource. We sequenced a total of 5499 Toxoplasma gondii parasites of three distinct strains. 4599 of the parasites were kept for analysis. Samples include Toxoplasma gondii RH tachyzoites, ME49 and Pru tachyzoites and bradyzoites in in vitro induction environment. Please note that the procesed data files generated from multiple samples are linked to the corresponding 'day 0' sample records.