Statistical methods for identification of NF-κB related genes and their expression profiles in channel catfish after bacterial infection

Abstract

Interactions of NF-κB family, IκB family and IKK complex are key components of NF-κB pathway that is essential for many biological processes including innate and adaptive immunity, and inflammation and stress responses. Despite their importance, systematic analysis of these genes in fish has been lacking. In this project, statistical analysis of NF-κB related genes and their gene expression after bacterial infection was conducted with channel catfish. A total of thirteen NF-κB related genes were identified in the channel catfish genome, including five NF-κB family genes, five IκB family genes and three IKK complex genes. To confirm the annotation of these thirteen NF-κB related genes, maximum likelihood methods were applied to construct phylogenetic tree of each gene with various species. The reliability of these constructed phylogenetic trees was confirmed by the bootstrap test. Syntenic analysis was used to further determine the annotation of those genes which failed to be confirmed by phylogenetic analysis. To determine the evolutionary patterns of these NF-κB related genes, likelihood ratio test was applied for detecting their selective pressures during evolution. The result indicates that negative selection may play a crucial role in the adaptive evolution of these NF-κB related genes. Expression profiles of NF-κB related genes after Flavobacterium columnare (columnaris) infection were determined by conducting both real-time PCR analysis of different tissues and Kal’s Z test with the existing RNA-Seq dataset. The majority of NF-κB related genes were significantly regulated in mucosal tissues of gill, skin and intestine after columnaris infection, indicating their potential involvement in host defense responses to bacterial infection. Distinct expression patterns of NF-κB related genes were observed in the susceptible and resistant catfish in response to columnaris infection, suggesting that expression of these genes may contribute to the variations in disease resistance/susceptibility of catfish.