AUTHOR=Sun Yujia , Luo Gang , Zhao Lingmin , Huang Lixing , Qin Yingxue , Su Yongquan , Yan Qingpi 

TITLE=Integration of RNAi and RNA-seq Reveals the Immune Responses of Epinephelus coioides to sigX Gene of Pseudomonas plecoglossicida

JOURNAL=Frontiers in Immunology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2018.01624

DOI=10.3389/fimmu.2018.01624

ISSN=1664-3224

ABSTRACT=<p><italic>Pseudomonas plecoglossicida</italic> is an important pathogen for aquaculture and causes high mortality in various marine fishes. Expression of <italic>sigX</italic> was found significantly up-regulated at 18°C than at 28°C, which was verified by quantitative real-time PCR (qRT-PCR). RNAi significantly reduced the content of <italic>sigX</italic> mRNA of <italic>P. plecoglossicida</italic>, whether in <italic>in vitro</italic> or in the spleen at all sampling time points. Compared with the wild-type strain, the infection of <italic>sigX</italic>-RNAi strain resulted in the onset time delay, and 20% reduction in mortality of <italic>Epinephelus coioides</italic>, as well as alleviates in the symptoms of <italic>E. coioides</italic> spleen. Compared with wild-type strain, the gene silence of <italic>sigX</italic> in <italic>P. plecoglossicida</italic> resulted in a significant change in transcriptome of infected <italic>E. coioides</italic>. The result of gene ontology and KEGG analysis on <italic>E. coioides</italic> showed that genes of serine-type endopeptidase and chemokine signaling pathway, coagulation and complement system, and intestinal immune network for IgA production pathway were mostly affected by <italic>sigX</italic> of <italic>P. plecoglossicida</italic>. Meanwhile, the immune genes were associated with different number of miRNA and lncRNA, and some miRNAs were associated with more than one gene at the same time. The results indicated that <italic>sigX</italic> was a virulent gene of <italic>P. plecoglossicida</italic>. The up-regulation of the immune pathways made <italic>E. coioides</italic> more likely to kill <italic>sigX</italic>-RNAi strain than the wild-type strain of <italic>P. plecoglossicida</italic>, while the immune genes were regulated by miRNA and lncRNA by a complex mode.</p>