Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes

Abstract

Resistance against diseases affects profitability of rainbow trout. Limited information is available about functions and mechanisms of teleost immune pathways. Immunogenomics provides powerful tools to determine disease resistance genes/gene pathways and develop genetic markers for genomic selection. RNA-Seq sequencing of the rainbow trout spleen yielded 93,532,200 reads (100 bp). High quality reads were assembled into 43,047 contigs. 26,333 (61.17%) of the contigs had hits to the NR protein database and 7024 (16.32%) had hits to the KEGG database. Gene ontology showed significant percentages of transcripts assigned to binding (51%), signaling (7%), response to stimuli (9%) and receptor activity (4%) suggesting existence of many immune-related genes. KEGG annotation revealed 2825 sequences belonging to “organismal systems” with the highest number of sequences, 842 (29.81%), assigned to immune system. A number of sequences were identified for the first time in rainbow trout belonging to Toll-like receptor signaling (35), B cell receptor signaling pathway (44), T cell receptor signaling pathway (56), chemokine signaling pathway (73), Fc gamma R-mediated phagocytosis (52), leukocyte transendothelial migration (60) and NK cell mediated cytotoxicity (42). In addition, 51 transcripts were identified as spleen-specific genes. The list includes 277 full-length cDNAs. The presence of a large number of immune-related genes and pathways similar to other vertebrates suggests that innate and adaptive immunity in fish are conserved. This study provides deep-sequence data of rainbow trout spleen transcriptome and identifies many new immune-related genes and full-length cDNAs. This data will help identify allelic variations suitable for genomic selection and genetic manipulation in aquaculture.

The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families

“…Moreover, 66 of those Siluriformes entries were from a single species, the American channel catfish ( Ictalurus punctatus ). These results contrast with other published transcriptome analysis of fish species that used BLASTX against the NCBI Non-redundant (Nr) database, reflecting the underrepresentation of Siluriformes sequences on more well curated databases (Ali et al, 2014; Zhenzhen et al, 2014). …”

A de novo transcriptome analysis shows that modulation of the JAK-STAT signaling pathway by salmonid alphavirus subtype 3 favors virus replication in macrophage/dendritic-like TO-cells

“…As for genes of the IFN receptor genes, IFNR1 and IFNR2 were expressed in both the TO-VS-IFN/SAV3 and TO-VS-SAV3 suggesting that activation of IFN-α/β receptors occurs as consequence of infection as well as IFN I treatment (as would be expected). However, it is important to point out that although our findings show the presence of both IFNR1 and IFNR2, which is in agreement with observations made by Ali et al [44] who reported the presence of both IFNR1 and IFNR2 based on a transcriptome analysis of rainbow trout spleen. Studies carried out by Sun et al [45] suggest that Atlantic salmon possess two clusters type I IFN receptor genes located on different chromosomes which allow for a large repertoire of IFN receptors than mammals and zebrafish.…”

A first insight into the spleen transcriptome of the notothenioid fish Lepidonotothen nudifrons: Resource description and functional overview

“…In teleost fish, spleen is an important secondary immune organ, related to innate and adaptive immunity, erythrocyte turnover and hemoglobin recycling (Ali et al, 2014). Environmental factors, such as temperature, constitute a strong adaptive trigger and are suspected to have left specific signatures in the immune response of animals inhabiting distinct regions (Windisch et al, 2012).…”