Characteristics of the long non-coding RNA-mRNA regulatory network in American eel (Anguilla rostrata) during Vibrio harveyi infection.

Vibrio harveyi is a highly pathogenic bacterium causing severe septicemia in American eel (Anguilla rostrata), yet the regulatory roles of long non-coding RNAs (lncRNAs) in the host immune response remain largely unexplored. In this study, American eels were challenged with V. harveyi, and kidney tissues were collected at 0-, 12-, 24-, 36-, 48 and 60-h post-infection (hpi) for bacterial load detection. Histopathological lesions and transcriptomic profiles (strand-specific RNA sequencing) were systematically analyzed at 0-, 24-, 36 and 48 hpi. Co-expression and co-location networks were constructed to identify interactions between differentially expressed (DE) lncRNAs and their target mRNAs. Bacterial load increased progressively, peaking at 48 hpi with a 100-fold higher load than at 12 hpi, accompanied by severe renal damage including tubular vacuolation and glomerular disintegration. Transcriptome analysis identified 76 shared DE-lncRNAs and 2230 shared DE-mRNAs across three infected time points from 24 to 48 hpi. Among these, 673 shared DE-mRNAs targeted by 60 shared DE-lncRNAs were significantly enriched in seven immune-related Gene Ontology (GO) terms and 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including complement activation, TNF signaling, and pathogen defense. Network analysis further revealed 24 key DE-lncRNAs that potentially regulate 600 DE-mRNAs via trans-acting mechanisms and 11 via cis-acting mechanisms. This study presents the first systematic characterization of lncRNA-mRNA regulatory networks in American eel during V. harveyi infection. The identified DE-lncRNAs and their target genes provide new insights into the molecular basis of host immune defense and offer potential targets for disease control in eel aquaculture.