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. 2018 Mar 20;19(1):211.
doi: 10.1186/s12864-018-4596-y.

Divergent transcriptomic responses underlying the ranaviruses-amphibian interaction processes on interspecies infection of Chinese giant salamander

Fei Ke  1 , Jian-Fang Gui  1 , Zhong-Yuan Chen  1 , Tao Li  1 , Cun-Ke Lei  1 , Zi-Hao Wang  1 , Qi-Ya Zhang  2
Affiliations

Divergent transcriptomic responses underlying the ranaviruses-amphibian interaction processes on interspecies infection of Chinese giant salamander

Fei Ke et al. BMC Genomics. .

Abstract

Background: Ranaviruses (family Iridoviridae, nucleocytoplasmic large DNA viruses) have been reported as promiscuous pathogens of cold-blooded vertebrates. Rana grylio virus (RGV, a ranavirus), from diseased frog Rana grylio with a genome of 105.79 kb and Andrias davidianus ranavirus (ADRV), from diseased Chinese giant salamander (CGS) with a genome of 106.73 kb, contains 99% homologous genes.

Results: To uncover the differences in virus replication and host responses under interspecies infection, we analyzed transcriptomes of CGS challenged with RGV and ADRV in different time points (1d, 7d) for the first time. A total of 128,533 unigenes were obtained from 820,858,128 clean reads. Transcriptome analysis revealed stronger gene expression of RGV than ADRV at 1 d post infection (dpi), which was supported by infection in vitro. RGV replicated faster and had higher titers than ADRV in cultured CGS cell line. RT-qPCR revealed the RGV genes including the immediate early gene (RGV-89R) had higher expression level than that of ADRV at 1 dpi. It further verified the acute infection of RGV in interspecies infection. The number of differentially expressed genes and enriched pathways from RGV were lower than that from ADRV, which reflected the variant host responses at transcriptional level. No obvious changes of key components in pathway "Antigen processing and presentation" were detected for RGV at 1 dpi. Contrarily, ADRV infection down-regulated the expression levels of MHC I and CD8. The divergent host immune responses revealed the differences between interspecies and natural infection, which may resulted in different fates of the two viruses. Altogether, these results revealed the differences in transcriptome responses among ranavirus interspecies infection of amphibian and new insights in DNA virus-host interactions in interspecies infection.

Conclusion: The DNA virus (RGV) not only expressed self-genes and replicated quickly after entry into host under interspecies infection, but also avoided the over-activation of host responses. The strategy could gain time for the survival of interspecies pathogen, and may provide opportunity for its adaptive evolution and interspecies transmission.

Keywords: Amphibian; Chinese giant salamander; Immune pathway; Interspecies infection; Ranavirus; Transcriptome response; Virus-host interactions.

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Conflict of interest statement

Ethics approval

Cultured CGSs were obtained from a farm in Jiangxi, China. The permission for collecting the specimens is not needed in the present study. The specimens are aquaculture animals. The animal procedure and protocol was approved by the Institutional Animal Care and Use Committee of the Institute of Hydrobiology, Chinese Academy of Sciences (Approval number: Y51317-1-301). The statements have been added in the ‘Ethics Approval and Consent to Participate’ section. All surgery was performed under the efforts made to minimize potential harmful effects.

Consent for publication

Not applicable

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Morphology and infection of RGV and ADRV. The ultrastructure of the viruses (RGV, ADRV). And the diseased animals were infected by their respective natural pathogen (RGV/frog, ADRV/Chinese giant salamander (CGS))
Fig. 2
Fig. 2
Expression of virus genes and number of DEGs (compared with control) in CGS. a number of paired reads covering genes of ADRV and RGV counted by featureCounts software. The Y-axes means the number of paired reads related to the genes. b Venn diagram of DEGs at 1 dpi or 7 dpi. Each circle represents a comparison that indicated in the cycle. Up- and down-regulated DEGs are indicated by “↑” and “↓”, respectively. Overlap region of two cycles represents DEGs in common
Fig. 3
Fig. 3
Replication of RGV and ADRV in GSTC cells. a the cytopathic effect (CPE) induced by RGV and ADRV in GSTC cells at different time points. b the one-step growth curves of RGV and ADRV in GSTC cells. The maximal titer of RGV is 106.9 TCID50/mL and that of ADRV is 106.1 TCID50/mL. c Ultrastructural observation of RGV and ADRV infected GSTC cells. The intracellular virus particles with crystalline aggregation were shown
Fig. 4
Fig. 4
Top 30 significantly enriched Go terms of DEGs (compared with control) in RGV-1d, ADRV-1d, RGV-7d, and ADRV-7d. The Go terms with blue font belonged to biological process (BP), with red font belonged to cellular component (CC), and black font belonged to molecular function (MF). Enrichment ratio was calculated with the formula: Sample number/Background number
Fig. 5
Fig. 5
Scatter plots of expression patterns of specific DEGs. DEGs in significantly enriched KEGG pathways related to immune response at 1 dpi (a) and 7 dpi (b) were selected for analysis. HCL: Hematopoietic cell lineage; TLR: Toll-like receptor signaling pathway; CCC: Complement and coagulation cascades; APP: Antigen processing and presentation; NKC: Natural killer cell mediated cytotoxicity. Each spot indicates a DEG. Key DEGs between ADRV and RGV groups were shown below the scatter plots with different font colors (blue font indicates RGV group and red font indicates ADRV group). Up-regulated DEGs were marked with “↑” and down-regulated DEGs were shown with “↓”. The genes that were detected by RT-qPCR were marked with “*”. Possible functions or targets of the pathway were indicated in dashed box
Fig. 6
Fig. 6
Significantly enriched DEGs in specific KEGG pathways. a MHC class I pathway of the KEGG pathway “Antigen processing and presentation” at 1 dpi. b coagulation cascades of the KEGG pathway “Complement and coagulation cascades” at 7 dpi. Enriched DEGs of the present study were marked with blue color (RGV) and red color (ADRV). Up- and down-regulated DEGs were marked with “↑” and “↓”, respectively
Fig. 7
Fig. 7
Experimental detection of expression of viral genes and host DEGs by RT-qPCR. Three genes from each virus and three host DEGs were selected for RT-qPCR. Expression levels of viral genes in RGV-1d sample and host genes in control sample were served as 1 in RT-qPCR analysis respectively. The primers and unigene IDs were shown in Additional file 8: Table S22
Fig. 8
Fig. 8
Illustration of CGS under interspecies and natural pathogen infection. Events occurred in RGV infection were shown in blue color and that related to ADRV was shown in red color. The events that proved in the present study were indicated by solid arrows, whereas that might occur were indicated by dotted arrows
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