Single-cell atlas in the living fossil Yangtze sturgeon provides insight into the evolution of fish

Abstract

Fish are the largest group of vertebrates. Studying the characteristics, functions, and interactions of different fish cells is important for understanding their roles in disease and evolution. However, most single cell RNA-seq studies in fish are restricted to a few specific organs, leaving a comprehensive cell landscape that aims to characterize the heterogeneity and connections among body-wide organs largely unexplored. We construct a single-cell atlas from the Yangtze sturgeon, Acipenser dabryanus, containing 82,401 high-quality cells and identify 72 major cell types. We compare differentially expressed genes among enterocytes in each part of the intestines and reveal the differences in absorption function of pyloric caecum, duodenum, spiral intestine, and rectum. Best4/Otop2 cells, newly identified in human, are also found in the intestines of sturgeon, indicating that these cells originated in an ancient period. We confirm the status of Müller glia as resident stem cells in fish nervous systems. We also characterize the different immune function between mucosa- and systemic-associated tissues. We detect several unexpected types of cells in Yangtze sturgeon, confirming that sturgeon is basal to teleosts. Cross-species analysis further indicates that sturgeon might occupy an ancient evolutionary position bridging the transition from cartilaginous to bony fish. In addition, novel cell markers, transcription factors, and intercellular communications are identified and found to be associated with the biological functions of specific types of cells. We generate the cellular landscape of an ancient fish and provide a valuable resource for revealing the cellular heterogeneity and biology of vertebrates.