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. 2023 Aug 18:14:1247038.
doi: 10.3389/fimmu.2023.1247038. eCollection 2023.

The transcriptome sequencing analysis reveals immune mechanisms of soybean fermented powder on the loach (Misgurnus anguillicaudatus) in response to Lipopolysaccharide (LPS) infection

Yayuan Xu  1   2 , Xinxin Zhang  3 , Dongqi Li  1   2 , Kun Qian  1   2 , Yu Liu  3 , Tingjuan Xu  4 , Lishang Dai  3 , Jianghua Cheng  1   2
Affiliations

The transcriptome sequencing analysis reveals immune mechanisms of soybean fermented powder on the loach (Misgurnus anguillicaudatus) in response to Lipopolysaccharide (LPS) infection

Yayuan Xu et al. Front Immunol. .

Abstract

The loach (Misgurnus anguillicaudatus), a small commercial fish that is widely cultivated for its high-quality protein, vitamins, minerals, and essential amino acid, is a member of the genus Misgurnus and the family Cyprinidae. In this study, we gave the LPS-injected loach fermented soybean meal and used transcriptome sequencing to investigate the impact of the fermented soybean powder on the loach's immune system. 3384 up-regulated genes and 12116 down-regulated genes were found among the 15500 differentially expressed genes, according to the results. The differentially expressed genes were shown to be involved in cellular processes, metabolic processes, cellular anatomical entities, and binding, according to the Go functional annotation. Meanwhile, the KEGG enrichment analysis indicated that the soybean fermented powder treated groups showed significant differences in DNA replication, Nucleotide excision repair, Fanconi anemia pathway, and Base excision repair pathways, suggesting that these pathways are closely related to the enhancement of the immune function of loach by soybean fermented powder. The particular conclusions not exclusively can provide a new conception for the rational utilization of soybean fermented powder but also can provide theoretical guidance for the subsequent healthy breeding of loach.

Keywords: LPS; immune function; loach; soybean fermentation powder; transcriptome sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Length distribution of Unigene. The abscissa indicates the length of assembled Unigenes, and the ordinate indicates the number of Unigenes under the corresponding length.
Figure 2
Figure 2
Distribution of Genes’ Coverage. Different colors in the graph represent the proportion of genes with a certain coverage range. (A) represents the gene coverage rate of Group A, and (B) represents the gene coverage rate of Group B.
Figure 3
Figure 3
Comparison of species quantity statistics chart.
Figure 4
Figure 4
KEGG pathway annotation.
Figure 5
Figure 5
KOG classification statistical chart.
Figure 6
Figure 6
GO secondary classification statistical chart. The results are summarized into three ontologies (Cellular Component, Biological Function and Molecular Function).
Figure 7
Figure 7
Differential gene statistical map. Abscissa: samples compared in pairs; Ordinate: the number of differentially expressed genes; Red represents up-regulated differential genes; Blue represents down-regulated differential genes.
Figure 8
Figure 8
Differential comparison volcano map. The abscissa represents the logarithmic value of the difference multiple between the two groups, and the ordinate represents the negative Log10 value of the difference FDR between the two groups. The red (up-regulated expression of Group B relative to Group A) and blue (down-regulated expression) dots indicate that the gene expression is different (the judging standard is FDR <0.05, and the difference multiple is more than twice), and the black dots indicate that there is no difference.
Figure 9
Figure 9
Column chart of GO enrichment classification. The abscissa is the secondary GOterm, and the ordinate is the number of differential genes in this term, with red indicating up-regulation and green indicating down-regulation.
Figure 10
Figure 10
KEGG enrichment bar chart. The top 20 pathways with the smallest Q value are used for drawing. The ordinate is the pathway, and the abscissa is the percentage of the pathway number to all the different genes. The darker the color, the smaller the Q value, and the values on the column are the pathway number and Q value.
Figure 11
Figure 11
qRT-PCR validation of RNA-seq results. The relative log2FoldChange is shown by the ordinate, and the gene is represented by the abscissa. Genes that are up-regulated are above the horizontal line, while those that are down-regulated are below it.
Figure 12
Figure 12
The qRT-PCR analysis of selected DEGs of the two groups. Data are presented as means ± SDs from three independent experiments. Student’s t-test was used for the statistical analysis between treated and untreated (control) samples in each rapeseed cultivar (**P < 0.01; ***P < 0.001). The abscissa represents the relative expression level, and the ordinate represents each gene. (A) shows up-regulated genes, and (B) shows down-regulated genes.
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