Spatiotemporal and single-cell atlases to dissect cell lineage differentiation and regional specific cell types in mouse ovary morphogenesis

Characterization of cell heterogeneity and molecular diversity using single-cell RNA sequencing has greatly enhanced our understanding of the ovary’s dynamic differentiation processes. However, regional specification of ovarian cells for certain physiological functions remains largely unexplored in the physical space. Here, we combine spatial transcriptomics with single-cell RNA sequencing technologies to build a spatiotemporal and single-cell atlas of ovaries from fetal to adult stages. We construct the pseudotime trajectories of female germ cells and bipotential pregranulosa cells and define key regulatory transcription factors responsible for their differentiation processes. Specifically, we dissect the relationships between two waves of meiosis initiation, oogenesis processes and folliculogenesis. Moreover, we characterize the region-specific subtypes of granulosa cells and luteal cells and construct pseudo-space-time trajectories from granulosa cells to luteal cells. Notably, we identify small luteal cells, a novel cell type, which highly express Onecut2 and exclusively locate at the corpus luteum. Altogether, this study comprehensively delineates ovary development and regional specific ovarian cell types.