For the first time, the comprehensive gene expression study provided valuable insights into the host-pathogen interaction between flounder (Paralichthys olivaceus) and Lymphocystis disease virus (LCDV) infection.

Lymphocystis disease virus (LCDV) infection may induce a variety of host gene expression changes associated with disease development; however, the understanding of the molecular mechanisms underlying host-virus interactions is limited.

The fish gill is an important tissue associated with immune responses, especially playing a crucial role in mucosal immunity as one of the mucosal barriers and gill tissue is susceptible to LCDV infection.  Moreover, two putative cellular receptors responsible for LCDV infection have been identified in flounder gill cells.

Thus, the transcriptome sequencing of flounder gill will promote the understanding of LCDV-host interactions and identify abundant immune-related genes in response to LCDV infection.

In the present study, RNA sequencing (RNA-Seq) was employed to investigate differentially expressed genes (DEGs) in the gill of the flounder (Paralichthys olivaceus) at one-week post-Lymphocystis disease virus (LCDV) infection.  

Transcriptome sequencing of the gill with and without LCDV infection was performed using the Illumina HiSeq 2500 platform. In total, RNA-seq analysis generated 193,225,170 clean reads aligned with 106,293 unigenes.

Among them, 1812 genes were up-regulated and 1626 genes were down-regulated after LCDV infection. The DEGs related to cellular process and metabolism occupied the dominant position involved in the LCDV infection.

A further function analysis demonstrated that the genes related to inflammation, the ubiquitin-proteasome pathway, cell proliferation, apoptosis, tumour formation, and anti-viral defence showed a differential expression.

Several DEGs including β actin, toll-like receptors, cytokine-related genes, antiviral related genes, and apoptosis-related genes were involved in LCDV entry and immune response. In addition, RNAseq data were validated by quantitative real-time PCR.

In conclusion, we studied the transcriptome responses of flounder gill to LCDV infection, and the results were anticipated to explain the molecular basis of early response of host to LCDV infection. The comprehensive gene expression study not only described for the first time the entire host responses to LCDV infection in the early infection phase, but also provided new information for identification of novel genes in flounder.