Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

  1. Keiichiro Koiwai  Is a corresponding author
  2. Takashi Koyama
  3. Soichiro Tsuda
  4. Atsushi Toyoda
  5. Kiyoshi Kikuchi
  6. Hiroaki Suzuki
  7. Ryuji Kawano
  1. Tokyo University of Marine Science and Technology, Japan
  2. Nagasaki University, Japan
  3. bitBiome Inc., Japan
  4. National Institute of Genetics, Japan
  5. University of Tokyo, Japan
  6. Chuo University, Japan
  7. 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.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Keiichiro Koiwai

    Laboratory of genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
    For correspondence
    koiwai@kaiyodai.ac.jp
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8890-8229
  2. Takashi Koyama

    Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
    Competing interests
    No competing interests declared.
  3. Soichiro Tsuda

    Research and Development Division, bitBiome Inc., Tokyo, Japan
    Competing interests
    Soichiro Tsuda, S.T. is an employee of bitBiome inc., and does not own any stock of the company..
  4. Atsushi Toyoda

    Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0728-7548
  5. Kiyoshi Kikuchi

    Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Japan
    Competing interests
    No competing interests declared.
  6. Hiroaki Suzuki

    Department of Precision Mechanics, Chuo University, Tokyo, Japan
    Competing interests
    No competing interests declared.
  7. Ryuji Kawano

    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
    Competing interests
    No competing interests declared.

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.

Reviewing Editor

  1. Jiwon Shim, Hanyang University, Republic of Korea

Version history

  1. Received: January 28, 2021
  2. Accepted: June 15, 2021
  3. Accepted Manuscript published: June 16, 2021 (version 1)
  4. Version of Record published: July 8, 2021 (version 2)

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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  1. Keiichiro Koiwai
  2. Takashi Koyama
  3. Soichiro Tsuda
  4. Atsushi Toyoda
  5. Kiyoshi Kikuchi
  6. Hiroaki Suzuki
  7. Ryuji Kawano
(2021)
Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process
eLife 10:e66954.
https://doi.org/10.7554/eLife.66954

Share this article

https://doi.org/10.7554/eLife.66954

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