Characterization of Rainbow Trout (Oncorhynchus mykiss) Spleen Transcriptome and Identification of Immune-Related Genes

Background: Resistance against specific diseases is affecting profitability in fish production systems including rainbow trout. Limited information is known about functions and mechanisms of teleosts immune pathways. Immunogenomics are powerful tools to determine disease resistance genes/gene pathways and develop genetic markers for marker-assisted selection.

Results: RNA-Seq sequencing of rainbow trout's spleen yielded 93,532,200 reads (100bp). After filtration, 58,013,135 (62%) high quality reads were assembled into 43,047 contigs. 26,334 (61.17%) contigs had hits to NR protein database and 7,024 (16.32%) had hits to KEGG database. Gene ontology showed significant percentage of transcripts assigned to binding (51%), metabolic processes (15%), signaling (7%), response to stimuli (9%) and receptor activity (4%) suggesting existence of many immune-related proteins in our data. KEGG annotation revealed 2,828 annotated sequences belonging to “organismal systems” with the highest number of sequences, 845 (29.88%), assigned to immune system. Number of annotated sequences, for the first time in rainbow trout, belonging to Toll-like, T-cell and B-cell receptor signaling pathways were 43, 68 and 60 respectively. Annotated contigs were analyzed by the online TargetIdentifier server. A total of 24 ,18 and 16 full-length and ORF completely-sequenced sequences were identified in Toll-like receptor signaling pathway, T-cell receptor signaling pathway and B-cell receptor signaling pathway respectively. Moreover, 51 transcripts were identified as spleen specific genes.

Conclusion: Presence of a large number of immune-related genes and pathways similar to other vertebrates suggests that innate and adaptive immunity in fish is conserved. Conversely, existence of a large group of genes that haven't previously identified in vertebrates suggests presence of fish-specific mechanisms/genes. This study provides deep-sequence data of rainbow trout's spleen transcriptome and identifies many new immune-related genes. In addition, it's helpful for identification of allelic variations suitable for applications of marker assisted selection and genetic manipulations in aquaculture.