- Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relyingFish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/M phi) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/M phi including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available.…
MetadatenAuthor details: | Lixing Huang, Ying Qiao, Wei Xu, Linfeng Gong, Rongchao He, Weilu Qi, Qiancheng Gao, Hongyan Cai, Hans-Peter GrossartORCiDGND, Qingpi YanORCiD |
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DOI: | https://doi.org/10.3389/fimmu.2021.737332 |
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ISSN: | 1664-3224 |
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Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/34646272 |
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Title of parent work (English): | Frontiers in immunology |
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Subtitle (English): | a reliable alternative for single-cell RNA-seq analysis in the spleen of teleost without reference genome |
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Publisher: | Frontiers Media |
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Place of publishing: | Lausanne |
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Publication type: | Article |
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Language: | English |
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Date of first publication: | 2021/09/27 |
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Publication year: | 2021 |
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Release date: | 2024/05/27 |
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Tag: | full-length transcriptome; immune cell population; infection; scRNA-seq; teleost |
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Volume: | 12 |
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Article number: | 737332 |
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Number of pages: | 18 |
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Funding institution: | Natural Science Foundation of Fujian ProvinceNatural Science Foundation of Fujian Province [2019J06020, 2019J01695]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [41502319]; Innovation Driven Development Foundation of Guangxi [AD19245135, AD19245161]; Doctoral Research Startup Fund of the Fourth Institute of Oceanography, Ministry of Natural Resources [201803, 201806]; Fund of Hainan Provincial Key Laboratory of Tropical Maricultural Technologies [TMTOF202104] |
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Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
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DDC classification: | 6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit |
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Peer review: | Referiert |
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Publishing method: | Open Access / Gold Open-Access |
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| DOAJ gelistet |
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License (German): | CC-BY - Namensnennung 4.0 International |
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