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. 2023 Jan 10:13:1039956.
doi: 10.3389/fimmu.2022.1039956. eCollection 2022.

Differentially expressed genes in head kidney of Pelteobagrus fulvidraco following Vibrio cholerae challenge

Sen-Hao Jiang  1   2 , Lin-Xin Wu  1 , Yu-Ting Cai  1 , Rui-Ting Ma  3 , Hua-Bin Zhang  1 , Dai-Zhen Zhang  1 , Bo-Ping Tang  1 , Qiu-Ning Liu  1 , Li-Shang Dai  2
Affiliations

Differentially expressed genes in head kidney of Pelteobagrus fulvidraco following Vibrio cholerae challenge

Sen-Hao Jiang et al. Front Immunol. .

Abstract

The yellow catfish (Pelteobagrus fulvidraco) is a freshwater fish with high economic value in eastern China. Nevertheless, pathogens causing bacterial diseases in P. fulvidraco have brought about huge economic loss and high mortality in artificial aquaculture. For disease control, it is critical to further understand the immune system of yellow catfish and immune-related genes with which they respond to pathogenic infections. In this study, high-throughput sequencing methods were used to analyze the transcriptomic spectrum of the head kidney from P. fulvidraco challenged by Vibrio cholera. A total of 45,544 unique transcript fragments (unigenes) were acquired after assembly and annotation, with an average length of 1,373 bp. Additionally, 674 differentially expressed genes (DEGs) were identified after stimulation with V. cholerae, 353 and 321 genes were identified as remarkably up- or downregulated, respectively. To further study the immune-related DEGs, we performed KEGG enrichment and GO enrichment. The results showed gene regulation of response to stimulus, immune response, immune system progress, response to external stimuli and cellular response to stimuli. Analysis of KEGG enrichment is important to identify chief immune related pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results indicated 10 immune response genes that were found to be upregulated compared to a control group after 6 h of V. cholerae challenging. In summary, the results of our study are helpful to determine the defense mechanisms and immune system responses of yellow catfish in reaction to bacterial challenges.

Keywords: Vibrio cholerae; differential expressed genes; immune response; pelteobagrus fulvidraco; transcriptome.

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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
The line plot shows the sequence length distribution of the unigenes and transcripts.
Figure 2
Figure 2
Annotated unigenes in seven databases.
Figure 3
Figure 3
Map of species distribution in the NR database.
Figure 4
Figure 4
Venn diagram of overlap of the seven databases.
Figure 5
Figure 5
Gene ontology classifications of assembled unigenes. A total of 17,372 unigenes were categorized into three functional categories: biological process, cellular component, and molecular function.
Figure 6
Figure 6
Function annotations of unigenes by KOG.
Figure 7
Figure 7
KEGG pathway assignment of the assembled unigenes. Different colored bars represent different groups.
Figure 8
Figure 8
Volcano plot of the differentially expressed genes in head kidney of yellow catfish.
Figure 9
Figure 9
Top 20 significantly enriched KEGG pathways of DEGs.
Figure 10
Figure 10
Validation of DEGs by qRT-PCR. The relative gene expression levels of 10 selected DEGs were examined. The β-actin gene was used as an internal standard. The means + SEM of three independent samples are shown (means ± SE, n = 3). Differences between treated and control samples were tested by one-way analysis of variance (ANOVA) followed by the Duncan’s new multiple range test. The P values are shown as *P < 0.05.
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