Cell lineage-resolved embryonic morphological map reveals novel signaling regulating cell fate and size asymmetry

Understanding the dynamic evolutions of cellular morphology throughout development is crucial for elucidating the mechanisms of morphogenesis and organogenesis. However, a systematic and detailed characterization of these processes poses a significant challenge. In this study, we introduce a comprehensive real-time morphological map covering over 95% of the cells produced during Caenorhabditis elegans embryogenesis, constituted by nearly 400,000 3D cell regions. Our map integrates information about identity, lineage, fate, shape, volume, surface area, and contact area for each individual cell, together with lineage-specific gene expression profiles, all of which are accessible through our custom-designed software and website. This morphological map enables vivid and precise characterization of key morphogenetic events, such as dorsal intercalation, intestinal morphogenesis, and body-wall muscle assembly. Furthermore, we reveal that the Notch and Wnt signaling pathways, in concert with mechanical forces from cell-cell interactions, orchestrate the asymmetry of both cell fate and cell size. Additionally, our analysis of cell-cell contact maps and lineage-specific gene expression profiles uncovers a cascade of Notch signaling events that drive the cell size asymmetries critical for kidney development. This resource lays the foundation for in-depth studies of the regulatory networks that determine cell fate, size, and cell cycle length throughout C. elegans embryogenesis.