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. 2023 Jan 17:13:1109606.
doi: 10.3389/fmicb.2022.1109606. eCollection 2022.

Comparative transcriptome analysis of rainbow trout gonadal cells (RTG-2) infected with U and J genogroup infectious hematopoietic necrosis virus

Jing-Zhuang Zhao  1   2   3 , Li-Ming Xu  2 , Guang-Ming Ren  2 , Yi-Zhi Shao  2 , Qi Liu  2 , Chun-Bo Teng  1 , Tong-Yan Lu  2
Affiliations

Comparative transcriptome analysis of rainbow trout gonadal cells (RTG-2) infected with U and J genogroup infectious hematopoietic necrosis virus

Jing-Zhuang Zhao et al. Front Microbiol. .

Abstract

Infectious hematopoietic necrosis virus (IHNV) is the causative pathogen of infectious hematopoietic necrosis, outbreaks of which are responsible for significant losses in rainbow trout aquaculture. Strains of IHNV isolated worldwide have been classified into five major genogroups, J, E, L, M, and U. To date, comparative transcriptomic analysis has only been conducted individually for the J and M genogroups. In this study, we compared the transcriptome profiles in U genogroup and J genogroup IHNV-infected RTG-2 cells with mock-infected RTG-2 cells. The RNA-seq results revealed 17,064 new genes, of which 7,390 genes were functionally annotated. Differentially expressed gene (DEG) analysis between U and J IHNV-infected cells revealed 2,238 DEGs, including 1,011 downregulated genes and 1,227 upregulated genes. Among the 2,238 DEGs, 345 new genes were discovered. The DEGs related to immune responses, cellular signal transduction, and viral diseases were further analyzed. RT-qPCR validation confirmed that the changes in expression of the immune response-related genes trpm2, sting, itgb7, ripk2, and irf1, cellular signal transduction-related genes irl, cacnb2, bmp2l, gadd45α, and plk2, and viral disease-related genes mlf1, mtor, armc5, pik3r1, and c-myc were consistent with the results of transcriptome analysis. Taken together, our findings provide a comprehensive transcriptional analysis of the differential virulence of the U and J genogroups of IHNV, and shed new light on the pathogenic mechanisms of IHNV strains.

Keywords: J genogroup; U genogroup; infectious hematopoietic necrosis virus; rainbow trout gonadal cells; transcriptome analysis (RNAseq).

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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
COG and GO function classification of unigenes from U-and J-IHNV-infected cells. (A) COG function classification of unigenes. (B) GO function classification of unigenes.
Figure 2
Figure 2
Comparison and enrichment analysis of DEGs in the Mock versus J-IHNV infection groups. (A) Volcano plot of DEGs. (B) Hierarchical clustering analysis of DEGs. (C) GO enrichment of DEGs. (D) KEGG enrichment analysis of DEGs.
Figure 3
Figure 3
Comparison and enrichment analysis of DEGs in the Mock versus U-IHNV infection groups. (A) Volcano plot of DEGs. (B) Hierarchical clustering analysis of DEGs. (C) GO enrichment of DEGs. (D) KEGG enrichment analysis of DEGs.
Figure 4
Figure 4
Comparison and enrichment analysis of DEGs in the U versus J-IHNV infection groups. (A) Volcano plot of DEGs. (B) Hierarchical clustering analysis of DEGs. (C) GO enrichment of DEGs. (D) KEGG enrichment analysis of DEGs.
Figure 5
Figure 5
DEG analysis of the U versus J-IHNV infection groups for genes related to immune responses, cellular signal transduction, and viral diseases. (A) Top 30 DEGs related to immune responses. (B) Top 40 DEGs related to cellular signal transduction. (C) Top 30 DEGs related to viral diseases.
Figure 6
Figure 6
Validation of selected DEGs related to immune responses, cellular signal transduction, and viral diseases. (A) DEG expression levels for genes related to immune responses. (B) DEG expression levels for genes related to cellular signal transduction. (C) DEG expression levels for genes related to viral diseases.
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