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

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Data availability
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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

1. Koiwai K
2. Koyama T
3. Tsuda S
4. Toyoda A
5. Kikuchi K
6. Suzuki H
7. Kawano R
(2020) Direct RNA sequencing data of hemocytes of Marsupenaeus japonicus using MinION
DDBJ Sequence Read Archive, DRA010948.

https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA010948
1. Koiwai K
2. Koyama T
3. Tsuda S
4. Toyoda A
5. Kikuchi K
6. Suzuki H
7. Kawano R
(2020) Raw sequence data of drop-seq on shrimp 1
DDBJ Sequence Read Archive, DRA010950.

https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA010950
1. Koiwai K
2. Koyama T
3. Tsuda S
4. Toyoda A
5. Kikuchi K
6. Suzuki H
7. Kawano R
(2020) Raw sequence data of drop-seq on shrimp 2
DDBJ Sequence Read Archive, DRA010951.

https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA010951
1. Koiwai K
2. Koyama T
3. Tsuda S
4. Toyoda A
5. Kikuchi K
6. Suzuki H
7. Kawano R
(2020) Raw sequence data of drop-seq on shrimp 3
DDBJ Sequence Read Archive, DRA010952.

https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA010952
1. Koiwai K
2. Koyama T
3. Tsuda S
4. Toyoda A
5. Kikuchi K
6. Suzuki H
7. Kawano R
(2020) Digital expression data of Drop-seq from three shrimp
DDBJ Genomic Expression Archive, E-GEAD-403.

ftp://ftp.ddbj.nig.ac.jp/ddbj_database/gea/experiment/E-GEAD-000/E-GEAD-403
1. Koiwai K
2. Koyama T
3. Tsuda S
4. Toyoda A
5. Kikuchi K
6. Suzuki H
7. Kawano R
(2020) Raw sequence data of drop-seq on mixture sample of HEK293 and 3T3 cells
DDBJ Sequence Read Archive, DRA010949.

https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA010949

The following previously published data sets were used

1. Koiwai K
2. Alenton RRR
3. Shiomi R
4. Nozaki R
5. Kondo H
6. Hirono I
(2016) Transcriptome analysis on different sub-populations of hemocytes of kuruma shrimp Marsupenaeus japonicus
DDBJ Sequence Read Archive, DRA004781.

https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA004781

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0002-8890-8229
Takashi Koyama

Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan

Competing interests
No competing interests declared.
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..
Atsushi Toyoda

Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-0728-7548
Kiyoshi Kikuchi

Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Japan

Competing interests
No competing interests declared.
Hiroaki Suzuki

Department of Precision Mechanics, Chuo University, Tokyo, Japan

Competing interests
No competing interests declared.
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.

Copyright

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.