show Abstracthide AbstractMany hard and soft corals harbor dinoflagellates of the Symbiodiniaceae family for photosynthesis. The algae live inside coral cells in a specialized membrane compartment called symbiosome, which share the photosynthetically fixed carbon with coral host cells, while host cells provide inorganic carbon for algal photosynthesis. This endosymbiotic relationship is critical for corals and increased environmental stresses are causing corals to expel their endosymbiotic algae, i.e. coral bleaching, lead to coral death and degradation of marine ecosystem. To date, the molecular pathways in coral cells that orchestrate algal recognition, uptake, and maintenance remain poorly understood. We report chromosome-level genome assembly of a fast-growing soft coral, Xenia species (sp.), and its use as a model to decipher the coral-algae endosymbiosis. Single cell RNA-sequencing (scRNA-seq) identified 13 cell types, including gastrodermis and cnidocytes, in Xenia sp.