Single-cell transcriptomics reveals the heterogeneous landscape of innate lymphoid cells in zebrafish

Innate lymphoid cells (ILCs) are a class of lymphocytes whose activation is independent of antigen receptors. Unlike mammals, where ILCs represent a small lymphoid subset, they are a dominant lymphocyte population in lower vertebrates and are thought to fulfill critical immunological roles in these animals. Yet their exact composition and functional activities remain largely uncharacterized. Here, using scRNA-seq, we identify a broad spectrum of distinct ILC subsets, including conventional subsets resembling their mammalian counterparts and unconventional ILC-like populations with unique features and distinct tissue distributions. We demonstrate that the complete ILC repertoire emerges early in development, independent of hematopoietic stem cells (HSCs), yet is maintained into adulthood via an HSC-dependent mechanism. Furthermore, we identify the essential role of interleukin-2 receptor beta (il2rβ) in zebrafish ILC-mediated immunity. Our work defines the landscape and ontogeny of zebrafish ILCs, revealing their underappreciated diversity and providing key insights into vertebrate innate immunity evolution.