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Background Cryptocaryonosis caused by  Cryptocaryon irritans  is one of the major diseases of large yellow croaker ( Larimichthys crocea ), which lead to massive economic losses annually to the aquaculture industry of  L. crocea . Although there have been some studies on the pathogenesis for cryptocaryonosis, little is known about the innate defense mechanism of different immune organs of large yellow croaker. Results In order to analyze the roles of long non-coding RNAs and genes specifically expressed between immune organs during the infection of  C. irritans , in this study, by comparing transcriptome data from different tissues of  L. crocea , we identified tissue-specific transcripts in the gills and skin, including 507 DE lncRNAs and 1592 DEGs identified in the gills, and 110 DE lncRNAs and 1160 DEGs identified in the skin. Furthermore, we constructed transcriptome co-expression profiles of  L. crocea  gill and skin, including 7,503 long noncoding RNAs (lncRNAs) and 23,172 protein-coding genes. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DEGs and the target genes of the DE lncRNAs in the gill were specifically enriched in several pathways related to immune such as HIF-1 signaling pathway. The target genes of DE lncRNAs and DEGs in the skin are specifically enriched in the complement and coagulation cascade pathways. Protein–protein interaction (PPI) network analysis identified 3 hub genes including  NFKBIA ,  TNFAIP3  and  CEBPB , and 5 important DE lncRNAs including MSTRG.24134.4, MSTRG.3038.5, MSTRG.27019.3, MSTRG.26559.1, and MSTRG.10983.1. The expression patterns of 6 randomly selected differentially expressed immune-related genes were validated using the quantitative real-time PCR method. Conclusions In short, our study is helpful to explore the potential interplay between lncRNAs and protein coding genes in different tissues of  L. crocea  post  C. irritans  and the molecular mechanism of pathogenesis for cryptocaryonosis. Highlights Skin and gills are important sources of pro-inflammatory molecules,and their gene expression patterns are tissue-specific after  C. irritans  infection. 15 DEGs and 5 DElncRNAs were identified as hub regulatory elements after  C. irritans  infection The HIF-1 signalingpathway and the complement and coagulation cascade pathway may be keytissue-specific regulatory pathways in gills and skin, respectively.

bmc genomics

Comparative transcriptome analysis reveals immunoregulation mechanism of lncRNA-mRNA in gill and skin of large yellow croaker (Larimichthys crocea) in response to Cryptocaryon irritans infection