Malaria is a devastating disease responsible for over 400,000 deaths each year. The disease is caused by a single-celled parasite of the genus Plasmodium, which establishes infection via a bite from an Anopheline mosquito. While the parasite progresses through a complex range of life stages, it is the blood stages, or the intraerythrocytic developmental cycle (IDC), that cause the large majority of harmful symptoms. During the course of the IDC, a parasite grows in size within a red blood cell until it is able to multiply itself asexually many times and burst from the cell as individual infectious units, each one then able to infect a new red blood cell and restart the cycle. This pattern of asexual reproduction and re-invasion of fresh cells allows the parasite population to swell to impressive sizes within a host.

While the IDC growth cycle can keep a parasite population happily established within the host, it is not able to allow passage between hosts. Thus, as the parasite progresses through the IDC, it must make a decision. Either it can continue into another cycle of asexual growth in that host, or sexually (and terminally) differentiate into gametocytes, the transmissible form of the parasite, and thus gain an opportunity to transfer to a new host. Gametocytogenesis, the formation of these sexual forms, is therefore essential for malaria transmission, and an attractive target for transmission blocking interventions. Despite its importance, we know little about sex-specific gene expression or how the decision to become male or female is made. Efforts to understand gametocytogenesis have been hampered by the fact that gametocytes often represent less than 1% of the total population of parasites circulating in a host, meaning any sexual transcriptional signal is lost amidst an abundance of asexuals. Single cell RNA-sequencing has revolutionised our ability to capture rare populations, providing an ideal window into heterogeneity between parasites and developmental processes at high resolution.

In this thesis, I use 10x Genomics single cell capture to sample the transcriptome of over 30,000 single cells from time points spanning the sexual developmental pathway of P. falciparum, from asexual growth, to sexual commitment, and into sexual maturity. I first use the data collected to generate a high quality reference atlas for gametocyte development. From this, I profile a number of global changes underlying sexual commitment, development, and maturity into males and females. By mixing two genetically distinct parasite strains (NF54 and 7G8), I place these findings in a larger context, describing differences in development that occur between strains of the same species. Lastly, I complete my profile of transcriptional changes underlying parasite development by exploring the localisation of the lesser profiled non-coding expression to specific regions of the life cycle, and how they may contribute to transmission.