Single-cell RNA sequencing reveals the immune cell landscape of head kidney in the Perciform fish (Micropterus salmoides)

Abstract

Teleost fish, a key transitional group in vertebrate evolution, possess immune systems that diverge substantially from those of mammals in structure, composition, and function. Within this group, the order Perciformes stands out for its ecological breadth, evolutionary significance, and value as a model for immunological research. However, the cellular complexity and developmental dynamics of their immune system remain insufficiently characterized. In this study, we employed single-cell RNA sequencing (scRNA-seq) to construct a comprehensive transcriptomic atlas of the head kidney in largemouth bass (Micropterus salmoides), a representative perciform species. We identified and annotated eight major hematopoietic and stromal cell populations, including hematopoietic stem/progenitor cells (HSPCs), erythrocytes (Eryt), granulocytes (Gran), macrophages (Mac), dendritic cells (DC), T and B cells, and mesenchymal stromal cells (MSCs). Subsequent analyses revealed extensive subpopulation heterogeneity across these lineages. We delineated early progenitor subsets, mapped B cell developmental trajectories, and characterized functionally distinct Mac and T cell subtypes. Notably, we identified Eryt cells exhibiting high MHC class II expression, supporting immunological roles beyond oxygen transport. A dot plot of core erythrocyte genes revealed largely lineage-restricted expression. However, several hemoglobin paralogs were also expressed in non-erythroid cells, suggesting functional divergence. Additionally, we identified a putative Gran-erythroid progenitor population and Mac subsets with distinct transcriptional profiles, underscoring the complexity, potential functionality, and wide diversity of specialized immune cell dynamics in Perciformes. Together, these findings significantly advance our understanding of teleost immune cell diversity and lineage specialization. The generated cell atlas provides a valuable resource and novel perspectives for deciphering fish immunity and hematopoiesis, advancing comparative immunology, and informing aquaculture health management.