Transcriptomics analysis reveals candidate genes and pathways for susceptibility or resistance to Singapore grouper iridovirus in orange-spotted grouper (Epinephelus coioides)

Abstract

In this study, the transcriptional response of grouper to Singapore grouper iridovirus (SGIV) stimulation was characterized using RNA sequencing. Transcriptome sequencing of three test groups in the grouper was performed using the Illumina MiSeq platform. The three test groups were a control group, which was injected with PBS buffer; a high-susceptible (HS) group, which died shortly after the SGIV injection; and a high-resistance (HR) group, which survived the SGIV injection. In total, 38,253 unigenes were generated. When the HS group was compared with the control group, 885 unigenes were upregulated and 487 unigenes were downregulated. When the HR and control groups were compared, 1114 unigenes were upregulated and 420 were downregulated, and when the HR and HS groups were compared, 1010 unigenes were upregulated and 375 were downregulated. In the KEGG analysis, two immune-related pathways, the p53 and peroxisome proliferator-activated receptor pathways, were detected with highly significant enrichment. In addition, 7465 microsatellites and 22,1569 candidate single nucleotide polymorphisms were identified from our transcriptome data. The results suggested several pathways that are associated with traits of disease susceptibility or disease resistance, and provided extensive information about novel gene sequences, gene expression profiles, and genetic markers. This may contribute to vaccine research and a breeding program against SGIV infection in grouper.

A chromosome‐level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth

“…As such, understanding the immune system and developing genomic selection programmes have become an important goal of grouper research. Recently, transcriptome analyses have been conducted to identify the candidate genes and pathways for susceptibility or resistance to virus infections (Tso & Lu, ; Yang et al, ). However, no genomic resource is available for groupers so far, severely hindering studies examining their phylogeny, evolution and biology.…”

Comparative Transcriptome Analysis Reveals the Molecular Immunopathogenesis of Chinese Soft-Shelled Turtle (Trionyx sinensis) Infected with Aeromonas hydrophila

“…The susceptible and resistant individuals in the natural population have offered excellent materials to study the molecular pathology or molecular basis of resistance for pathogenic diseases in many animal species [ 40 , 41 ]. In livestock and poultry animals, for example, comparative transcriptomes were analyzed to reveal the molecular mechanism differences in response to Mycoplasma hyopneumoniae infection in two pig breeds [ 42 ].…”

Combining Multiple Approaches and Models to Dissect the Genetic Architecture of Resistance to Infections in Fish

“…Transcriptome responses to the infection were also analyzed in resistant and susceptible fish to a few other viruses: VHSV in rainbow trout (Verrier et al, 2018, see below), herpesvirus CaHV in gibel carp (Gao et al, 2017;Mou et al, 2018), ISAV in Atlantic salmon (Dettleff et al, 2017), and Singapore grouper iridovirus in orange-spotted grouper (Yang et al, 2019). Similar approaches were also followed with fish showing contrasted levels of resistance to parasites.…”