RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus

Genome-wide identification of Hsp70 genes in channel catfish and their regulated expression after bacterial infection

“…In this study, we identified a full set of 57 catfish Hsp40 genes in the catfish genome. This was achieved by thorough analysis of rich genomic and transcriptomic resources including several hundred thousands of ESTs [33][34][35], RNA-Seq transcriptome assemblies [37,38], and the draft genome sequences (unpublished). Phylogenetic and syntenic analyses allowed annotation of Hsp40 genes.…”

“…The Illumina-based RNA-Seq reads were retrieved from bacterial challenge experiments in catfish: intestine samples challenged with Edwardsiella ictaluri (SRA accession number SRP009069) [34], liver samples challenged with E. ictaluri challenge (SRA number SRP028159) [33] and gill samples challenged with Flavobacterium Columnare (SRA number SRP012586) [35]. Trimmed highquality reads were mapped onto the catfish Hsp40 genes using CLC Genomics Workbench software (version 5.5.2; CLC bio, Aarhus, Denmark).…”

“…In our recent RNASeq studies, we have successfully obtained comprehensive transcriptome assemblies from catfish intestine and liver after E. ictaluri infection and from catfish gill after F. Columnare infection [33][34][35]. The expression patterns of differentially expressed genes from these three studies were validated by quantitative real-time RT-PCR with average correlation coefficient around 0.9 (p,0.001).…”

An Overview of the Immunological Defenses in Fish Skin

“…While these mechanisms have been the intense focus of microbiologists for decades, only recently have tools been developed to allow the capture of molecular signatures related to host responses and host-pathogen interactions during infection [352]. Using Illumina RNA-seq technology, channel catfish transcriptomic responses in the intestine following challenge with the Gram-negative bacterium Edwardsiella ictaluri have been studied for the first time [352]. The technology has allowed studying a broad representation of catfish genes (including previously unsequenced transcripts) and accurately quantifying transcript levels of 1633 differentially expressed genes.…”

“…New technologies based on gene study will reveal novel patterns of teleost mucosal gene expression and will highlight unexpected roles for candidate genes and pathways. Utilization of these findings will improve strategies for selection of disease-resistant broodstock and evaluation of prevention and treatment options [352]. Different assays have also been developed for the measurement of differential real-time expression of immune-related genes in skin after natural or experimental infections.…”