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

Keiichiro Koiwai; Phattarunda Jaree; Kanjanaporn Nanthajak; Masachika Harada; Hiroki Kusaka; Ammara Sinprasertporn; Hajime Yuasa; Kayo Konishi; Reiko Nozaki; Hidehiro Kondo; Jumroensri Thawonsuwan; Kunlaya Somboonwiwat; Ikuo Hirono

doi:10.1016/j.fsi.2026.111178

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

Fish Shellfish Immunol. 2026 Feb 2:111178. doi: 10.1016/j.fsi.2026.111178. Online ahead of print.

Authors

Affiliations

¹ Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan, Minato-ku, Tokyo, Japan. Electronic address: koiwai@kaiyodai.ac.jp.
² Center of Applied Shrimp Research and Innovation, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand.
³ Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
⁴ Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan, Minato-ku, Tokyo, Japan.
⁵ Songkhla Aquatic Animal Health Research Center, Department of Fisheries, Songkhla, Thailand.
⁶ Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand. Electronic address: Kunlaya.S@chula.ac.th.

PMID: 41638371
DOI: 10.1016/j.fsi.2026.111178

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.