Co-Expression Network Analysis of Spleen Transcriptome in Rock Bream (Oplegnathus fasciatus ) Naturally Infected with Rock Bream Iridovirus (RBIV)

International Journal of Molecular Sciences
Ahran KimDo-Hyung Kim

Abstract

Rock bream iridovirus (RBIV) is a notorious agent that causes high mortality in aquaculture of rock bream (Oplegnathus fasciatus). Despite severity of this virus, no transcriptomic studies on RBIV-infected rock bream that can provide fundamental information on protective mechanism against the virus have been reported so far. This study aimed to investigate physiological mechanisms between host and RBIV through transcriptomic changes in the spleen based on RNA-seq. Depending on infection intensity and sampling time point, fish were divided into five groups: uninfected healthy fish at week 0 as control (0C), heavy infected fish at week 0 (0H), heavy mixed RBIV and bacterial infected fish at week 0 (0MH), uninfected healthy fish at week 3 (3C), and light infected fish at week 3 (3L). We explored clusters from 35,861 genes with Fragments Per Kilo-base of exon per Million mapped fragments (FPKM) values of 0.01 or more through signed co-expression network analysis using WGCNA package. Nine of 22 modules were highly correlated with viral infection (|gene significance (GS) vs. module membership (MM) |> 0.5, p-value < 0.05). Expression patterns in selected modules were divided into two: heavy infected (0H and 0MH) and control and light-...Continue Reading

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Datasets Mentioned

BETA
PRJNA511555

Methods Mentioned

BETA
RNA-seq
nuclear magnetic resonance
metabolomics profiling
proteomic profiling
PCR

Software Mentioned

BLASTx Automatic Annotation Server ( KAAS
R
RNA
KEGG Automatic Annotation Server ( KAAS ) Gene Ontology ( BiNGO )
- Expectation Maximization ( RSEM )
seq TM
BLASTx
WGCNA
DEGES edgeR
Tag Count Comparison ( TCC )

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