Single-cell transcriptome sequencing analysis of physiological and immune profiling of crucian carp (Carassius auratus) gills

Gills are the main respiratory organs of fish and bear important physiological and immunological functions, but the functional heterogeneity of interlamellar cell mass (ILCM) at the single-cell level has rarely been reported. Here, we identified 19 cell types from the gills of crucian carp (Carassius auratus) by single-cell RNA sequencing (scRNA-seq) in combination with histological analysis. We annotated ILCM and analyzed its functional heterogeneity at the single-cell level for the first time. Functional enrichment analysis and cell cycle analysis identified ILCM as a type of metabolically active cells in a state of constant proliferation, and identified the major pathways responsible for ILCM immunoregulation. Histological analysis revealed the morphology and positional relationships of 6 cell types. Meanwhile, the gene regulatory network of ILCM was established through weighted gene co-expression network analysis (WGCNA), and one transcription factor and five hub genes related to immunoregulation were identified. We found that pyroptosis might be an important pathway responsible for the immune response of ILCM. Our findings provide an insight into the physiological and immune functions of gills and ILCM at the single-cell level and lay a solid foundation for further exploration of the molecular mechanism of ILCM immunity functions. •Single-cell interlamellar cell mass (ILCM) was annotated in Carassius auratus gills.•Pyroptosis may be an important pathway for ILCM immune response.•Crucian carp gill profiles were plotted using single-cell transcriptome sequencing.