RNA-Seq transcriptome analysis of the olive flounder ( Paralichthys olivaceus ) kidney response to vaccination with heat-inactivated viral hemorrhagic septicemia virus

Hwang, Jee Youn; Kwon, Mun Gyeoung; Jung, Sung‐Hee; Park, Myoung Ae; Kim, Dong-Wook; Cho, Wang Sik; Park, Jeong Woo; Son, Maeng-Hyun

doi:10.1016/j.fsi.2017.01.016

Cited by 27 publications

(9 citation statements)

References 39 publications

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“…Being qualitative as well as quantitative, this technology has led to the identification of many molecular actors and their patterns of expression in a limited time-frame, laying the foundation for further studies in the mechanisms of host–pathogen interaction. This technology has also aided in testing the efficacy of vaccines [ 41 , 44 , 74 ], treatment options [ 107 , 114 ], immunostimulants [ 150 ], and immunoprotective diets [ 36 ] against pathogens. Transcriptome data derived during host–pathogen interactions will be useful to understand virulence genes of the pathogens that are induced in vivo.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

Sudhagar

Kumar

El-Matbouli

2018

IJMS

130

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In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.

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Section: Discussionmentioning

confidence: 99%

“…RNA-Seq analysis of the kidney of the olive flounder ( Paralichthys olivaceus ) revealed that heat-inactivated vaccination against VHSV modulates numerous genes involved in the acute phase response, TLR, IFN, and apoptosis pathways [ 74 ]. Poly (I:C) is an immunostimulant often used as a viral mimic.…”

Section: Fish Immune Response To Viral Pathogensmentioning

confidence: 99%

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

Sudhagar

Kumar

El-Matbouli

2018

IJMS

130

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“…With development of sequencing technique, numerous genomic researches have been reported to understand infection results by virus 28,31,40 , bactria 26,41,42 , and parasite 43 in the olive flounder genome. A fundamental way to overcome disease outbreak from external pathogens is to approach from their genome level.…”

Section: Discussionmentioning

confidence: 99%

“…With development of wide-sized analysis methods, it is not difficult to figure out change of gene expression level after any chemical treatment or environmental change. Recently, studies to identify large-scale genes were conducted in the olive flounder genome for researches about vaccine, gonadal development, and sex determination [28][29][30] . In particular, characterizing of immune-related genes was reported in olive flounder spleen tissue 31 .…”

mentioning

confidence: 99%

Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus)

Nam

Mishra

Gim³

et al. 2018

Sci Rep

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Olive flounder (Paralichthys olivaceus) is one of economically valuable fish species in the East Asia. In comparison with its economic importance, available genomic information of the olive flounder is very limited. The mass mortality caused by variety of pathogens (virus, bacteria and parasites) is main problem in aquaculture industry, including in olive flounder culture. In this study, we carried out transcriptome analysis using the olive flounder gill tissues after infection of three types of pathogens (Virus; Viral hemorrhagic septicemia virus, Bacteria; Streptococcus parauberis, and Parasite; Miamiensis avidus), respectively. As a result, we identified total 12,415 differentially expressed genes (DEG) from viral infection, 1,754 from bacterial infection, and 795 from parasite infection, respectively. To investigate the effects of pathogenic infection on immune response, we analyzed Gene ontology (GO) enrichment analysis with DEGs and sorted immune-related GO terms per three pathogen groups. Especially, we verified various GO terms, and genes in these terms showed down-regulated expression pattern. In addition, we identified 67 common genes (10 up-regulated and 57 down-regulated) present in three pathogen infection groups. Our goals are to provide plenty of genomic knowledge about olive flounder transcripts for further research and report genes, which were changed in their expression after specific pathogen infection.

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“…Previously, many genome-wide analyses have been conducted to determine immune response to novirhabdoviruses in olive flounder [86,99,[101][102][103][104][105][106][107], rainbow trout (Oncorhynchus mykiss) [108], sockeye salmon (Oncorhynchus nerka) [109], and turbot (Scophthalmus maximus) [86] and identified a large number of immune response genes modulated by novirhabdovirus infection. Of the 9 genes commonly modulated by three novirhabdoviruses, consistent with our data, genome-wide analyses identified TLR1 [93] and TLR2 [80] as being modulated by VHSV infection.…”

Section: Plos Onementioning

confidence: 99%

Transcriptome analysis based on RNA-seq of common innate immune responses of flounder cells to IHNV, VHSV, and HIRRV

et al. 2020

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Viral hemorrhagic septicemia virus (VHSV) and hirame rhabdovirus (HIRRV) belong to the genus Novirhabdovirus and are the causative agents of a serious disease in cultured flounder. However, infectious hematopoietic necrosis virus (IHNV), a prototype of the genus Novirhabdovirus, does not cause disease in flounder. To determine whether IHNV growth is restricted in flounder cells, we compared the growth of IHNV with that of VHSV and HIRRV in hirame natural embryo (HINAE) cells infected with novirhabdoviruses at 1 multiplicity of infection. Unexpectedly, we found that IHNV grew as well as VHSV and HIRRV. For successful growth in host cells, viruses modulate innate immune responses exerted by virus-infected cells. Our results suggest that IHNV, like VHSV and HIRRV, has evolved the ability to overcome the innate immune response of flounder cells. To determine the innate immune response genes of virus-infected HINAE cells which are commonly modulated by the three novirhabdoviruses, we infected HINAE cells with novirhabdoviruses at multiplicity of infection (MOI) 1 and performed an RNA sequencing-based transcriptome analysis at 24 h post-infection. We discov-ered~12,500 unigenes altered by novirhabdovirus infection and found that many of these were involved in multiple cellular pathways. After novirhabdovirus infection, 170 genes involved in the innate immune response were differentially expressed compared to uninfected cells. Among them, 9 genes changed expression by more than 2-fold and were commonly modulated by all three novirhabdoviruses. Interferon regulatory factor 8 (IRF8), C-X-C motif chemokine receptor 1 (CXCR1), Toll/interleukin-1 receptor domain-containing adapter protein (TIRAP), cholesterol 25-hydroxylase (CH25H), C-X-C motif chemokine ligand 11, duplicate 5 (CXCL11.5), and Toll-like receptor 2 (TLR2) were up-regulated, whereas CC motif chemokine receptor 6a (CCR6a), interleukin-12a (IL12a), and Toll-like receptor 1 (TLR1) were down-regulated. These genes have been reported to be involved in antiviral responses and, thus, their modulation may be critical for the growth of novirhabdovirus in flounder cells. This is the first report to identify innate immune response genes in flounder that are commonly modulated by IHNV, VHSV, and HIRRV. These data will provide new insights into how novirhabdoviruses survive the innate immune response of flounder cells.

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RNA-Seq transcriptome analysis of the olive flounder ( Paralichthys olivaceus ) kidney response to vaccination with heat-inactivated viral hemorrhagic septicemia virus

Cited by 27 publications

References 39 publications

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus)

Transcriptome analysis based on RNA-seq of common innate immune responses of flounder cells to IHNV, VHSV, and HIRRV

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