Bioinformatics identification of induced genes in Marsupenaeus japonicus in response to injection of long non-specific dsRNA and their association with immunity against white spot syndrome virus (WSSV)

Document Type : Research Paper

Authors

1 Assistant Professor, Iranian Shrimp Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education & Extension Organization (AREEO), Bushehr, Iran.

2 Assistant Professor, Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran

10.22103/jab.2025.24530.1638

Abstract

Abstract
Objective
The sustainable development of the farmed shrimp industry is threatened by a wide range of important pathogens, including white spot syndrome virus (WSSV), which causes severe economic losses to the industry. The aim of this study was to identify differentially expressed genes (DEGs) in Kuruma shrimp (Marsupenaeus japonicus) in response to injection of long non-specific dsRNA and their association with survival and immunity against white spot disease (WSD).
Materials and methods
Eight microarray data from shrimp hemocytes injected with PBS and long non-specific dsRNA (four samples from each group) at time intervals of 24 and 48 hours after injection were extracted from the GEO database with accession number GSE61541 and analyzed using the GEO2R tool. After automatic normalization, the data were imported into Excel software and differentially expressed genes (DEGs) were identified with an adjusted P-Value less than 0.05. Genes with LogFC greater than 2 and less than -2 were considered as up- and down-expressed genes, respectively. Then, the commen DEGs were identified using the VENNY 2.0.2 tool.
Results
Data analysis showed that 160 DEGs were identified in 24 hours after dsRNA injection, of which 111 genes were up-regulated and 49 genes down-regulated. As well as, the results showed that 206 DEGs were identified in 48 hours after dsRNA injection, of which 138 genes were up-regulated and 68 genes down-regulated. The analysis of DEGs using the VENNY tool showed that 74 common genes were identified in 24 and 48 hours after dsRNA injection, of which 67 genes were up-regulated and 7 genes down-regulated. Shrimp injected with dsRNA had a higher number of DEGs than the PBS-injected group, most of which were up-regulated. The results of this study confirmed that injection of long non-specific dsRNAs could induce many genes related to innate immunity, such as Ribonuclease T2, C-type lectin 2, HSP90, Caspase Nc-like, and TRIM64 in response to WSSV infection in Kuruma shrimp.
Conclusions
Various biological functions were predicted for genes induced in Kuruma shrimp in response to injection of long non-specific dsRNA included recognition of pathogen-associated molecular patterns (PAMPs), binding, homeostasis, apoptosis, catalytic, transmembrane, chaperone and RNAi. Identification of these genes could be useful in finding markers associated with white spot infection, diagnosis, or designing inhibitors against that disease.
Keywords: Innate immunity, RNA interference (RNAi), Microarray, Kuruma shrimp (Marsupenaeus japonicas), White spot syndrome virus (WSSV)

Keywords

References

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Agricultural Biotechnology Journal
Volume 17, Issue 2
May 2025
Pages 237-262

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