Single-cell RNA sequencing reveals cellular heterogeneity and gonadal niche interactions in the hermaphroditic scallop Argopecten irradians

The process of gonadal development necessitates the self-renewal and differentiation of germ cells, which is a complex and precisely regulated procedure that is inextricably linked with the gonadal microenvironment. However, our understanding of the microenvironment of the gonads remains incomplete in invertebrates. In the present study, we employed single-cell transcriptome sequencing to examine the early differentiated gonad of a simultaneous hermaphroditic scallop, Argopecten irradians . A total of six clusters were identified, comprising 5669 high-quality cells. The clusters were classified into one germ cell cluster and five somatic cell clusters (accessory cell, hemocyte, ciliated cell, fibroblast, and an uncharacterized cluster) based on functional enrichment analysis and the identification of classical marker genes. The cell types were validated through in situ hybridization. In addition, a weighted gene co-expression network analysis (WGCNA) was employed to elucidate the co-expression patterns of these clusters, which identified key transcription factors in these modules (e.g., Hr38 , Mycbp , and Nkx2.5 ) and revealed that germ cells exhibited a high degree of connectivity with accessory cells. Further analysis demonstrated the existence of two subsets of germ cells with a continuous developmental trajectory and three subclusters of accessory cells, including an ovary-unique cell type. A substantial number of bidirectional ligand–receptor interactions were observed between germ cells and accessory cells, including those involving the TGF-β, Notch, PI3K-Akt, and Wnt signaling pathways. Our study elucidates the cellular composition and gonadal microenvironment of A. irradians at the single-cell level, thereby providing new insights into a comprehensive understanding of the development of germ cells in bivalve mollusks. • A germ cell cluster and five somatic cell clusters were identified in scallop gonads. • There are two subsets of germ cells with a continuous developmental trajectory. • There are three subclusters of accessory cells including an ovary-unique cell type. • Key transcription factors such as Hr38 , Mycbp , and Nkx2.5 were identified. • Scallop gonadal niche interactions involve TGF-β, Notch, PI3K-Akt, and Wnt pathways.