TY  - JOUR
A1  - Huang, Lixing
A1  - Qiao, Ying
A1  - Xu, Wei
A1  - Gong, Linfeng
A1  - He, Rongchao
A1  - Qi, Weilu
A1  - Gao, Qiancheng
A1  - Cai, Hongyan
A1  - Grossart, Hans-Peter
A1  - Yan, Qingpi
T1  - Full-length transcriptome
BT  - a reliable alternative for single-cell RNA-seq analysis in the spleen of teleost without reference genome
JF  - Frontiers in immunology
N2  - 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 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.
KW  - scRNA-seq
KW  - full-length transcriptome
KW  - immune cell population
KW  - teleost
KW  - infection
Y1  - 2021
U6  - https://doi.org/10.3389/fimmu.2021.737332
SN  - 1664-3224
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  -