Single-cell RNA-seq reveals cellular dynamics and emergency hematopoiesis in banana shrimp Penaeus merguiensis hemocytes upon Yellow Head Virus infection

Abstract

As global aquaculture of penaeid shrimp expands, the banana shrimp (Penaeus merguiensis) has gained attention as a promising sustainable alternative to the non-native P. vannamei. However, its cellular immune response to major pathogens like yellow head virus (YHV) remains poorly understood, limiting effective disease management. In this study, we established a comprehensive reference transcriptome for P. merguiensis by integrating data from 13 major tissues and conducted single-cell RNA sequencing (scRNA-seq) on hemocytes under normal and YHV-infected conditions. We identified eight distinct hemocyte clusters (cluster 0–7) and demonstrated that YHV infection triggers a massive turnover of the hemocyte landscape. Specifically, mature immune-active clusters expressing anti-lipopolysaccharide factors (ALFs) and lysozymes were significantly depleted, likely due to virus-induced apoptosis. Conversely, a marked expansion of an immature hemocyte progenitor cluster (cluster 4) was observed, indicating a host-driven emergency hematopoiesis response. Our analysis further revealed that global transcriptional changes are heavily biased by these composition shifts: 30.7% of the total 114 globally regulated genes were identified as cluster-specific markers. These findings provide a high-resolution model of crustacean immune dynamics and highlight the necessity of single-cell analysis for accurately deciphering host-pathogen interactions.