@article {Xue656165, author = {Yuan Xue and Terence C. Theisen and Suchita Rastogi and Abel Ferrel and Stephen R. Quake and John C. Boothroyd}, title = {A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression}, elocation-id = {656165}, year = {2020}, doi = {10.1101/656165}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2020/02/16/656165}, eprint = {https://www.biorxiv.org/content/early/2020/02/16/656165.full.pdf}, journal = {bioRxiv} }