Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process
- Tokyo University of Marine Science and Technology, Japan
- Nagasaki University, Japan
- bitBiome Inc., Japan
- National Institute of Genetics, Japan
- University of Tokyo, Japan
- Chuo University, Japan
- Tokyo University of Agriculture and Technology, Japan
Abstract
Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles. Our present study using single-cell RNA sequencing, revealed six types of hemocytes of Marsupenaeus japonicus based on their transcriptional profiles. We identified markers of each subpopulation and predicted the differentiation pathways involved in their maturation. We also predicted cell growth factors that might play crucial roles in hemocyte differentiation. Different immune roles among these subpopulations were suggested from the analysis of differentially expressed immune-related genes. These results provide a unified classification of shrimp hemocytes, which improves the understanding of its immune system.
Data availability
Sequencing data have been deposited in DDBJ under accession codes DRA010948, DRA010949, DRA010950, DRA010951, and DRA010952.Digital expression data of Drop-seq from three shrimp were archived in DDBJ under accession code E-GEAD-403.Data code can be accessed at https://github.com/KeiichiroKOIWAI/Drop-seq_on_shrimp.All data generated or analyzed during this study are included in the manuscript and supporting files.All tables are provided as Supplementary files.Source data files are provided to support the sinaplots in Figure 2, Figure 2-figure supplement 1.Source data files are provided to support thepercentage of cell state in Figure 5.Source data file is provided to support the bar graph in Figure 9F.
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Direct RNA sequencing data of hemocytes of Marsupenaeus japonicus using MinIONDDBJ Sequence Read Archive, DRA010948.
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Raw sequence data of drop-seq on shrimp 1DDBJ Sequence Read Archive, DRA010950.
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Raw sequence data of drop-seq on shrimp 2DDBJ Sequence Read Archive, DRA010951.
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Raw sequence data of drop-seq on shrimp 3DDBJ Sequence Read Archive, DRA010952.
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Digital expression data of Drop-seq from three shrimpDDBJ Genomic Expression Archive, E-GEAD-403.
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Raw sequence data of drop-seq on mixture sample of HEK293 and 3T3 cellsDDBJ Sequence Read Archive, DRA010949.
Article and author information
Author details
Funding
Japan Society for the Promotion of Science (20K15603)
- Keiichiro Koiwai
Japan Society for the Promotion of Science (19J00539)
- Keiichiro Koiwai
Japan Society for the Promotion of Science (17H06425)
- Kiyoshi Kikuchi
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Koiwai et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process
eLife 10:e66954.
https://doi.org/10.7554/eLife.66954
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