PT - JOURNAL ARTICLE AU - Yuan Xue AU - Terence C. Theisen AU - Suchita Rastogi AU - Abel Ferrel AU - Stephen R. Quake AU - John C. Boothroyd TI - A single-parasite transcriptional atlas of <em>Toxoplasma gondii</em> reveals novel control of antigen expression AID - 10.1101/656165 DP - 2020 Jan 01 TA - bioRxiv PG - 656165 4099 - http://biorxiv.org/content/early/2020/02/16/656165.short 4100 - http://biorxiv.org/content/early/2020/02/16/656165.full AB - 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 &gt;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.