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

item ALI, ALI - Middle Tennessee State University
item THORGAARD, GARY - Washington State University
item Rexroad, Caird
item YAO, JIANBO - West Virginia University
item SALEM, MOHAMED - Middle Tennessee State University

Submitted to: Frontiers in Livestock Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2014
Publication Date: 10/14/2014
Citation: Ali, A., Thorgaard, G., Rexroad III, C.E., Yao, J., Salem, M. 2014. Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes. Frontiers in Livestock Genomics. 5:348. DOI: 10.3389/fgene.2014.00348.

Interpretive Summary: The spleen is known to be an important immune organ in vertebrates, including fish species such as rainbow trout. We obtained gene sequence information from rainbow trout spleens for comparison with similar information from better studied species. Specifically, 93,532,200 partial gene sequences were obtained and analyzed to identify immune related genes and biochemical processes in the rainbow trout. This resource will aid in identifying genes that underlie resistance to disease affecting aquaculture production efficiency.

Technical Abstract: Disease susceptibility affects production efficiency and profitability in rainbow trout aquaculture. There is limited information available regarding the functions and mechanisms of teleost immune pathways. Immunogenomics provides powerful approaches to identify disease resistance genes/gene pathways and develop genetic markers that can be employed in breeding strategies for genetic improvement. RNA-Seq analysis of the rainbow trout spleen yielded 93,532,200 reads (100bp). High quality reads were assembled into 43,047 contigs. 26,334 (61.17%) contigs had hits to the NR protein database and 7,024 (16.32%) had hits to the KEGG database. Gene ontology showed significant percentages of transcripts assigned to binding (55.17%), signaling (14.93%), response to stimuli (12.21%) and receptor activity (7.41%); suggesting existence of many immune-related genes. KEGG annotation revealed 2,828 sequences belonging to “organismal systems” with the highest number of sequences, 845 (29.88%), assigned to immune system. A number of sequences were annotated for the first time in rainbow trout belonging to Toll-like receptor signaling (43), T-cell (70) and B-cell receptor signaling (60), chemokine signaling pathway (91), Fc gamma R-mediated phagocytosis (61), leukocyte transendothelial migration (66) and NK cell mediated cytotoxicity (48). The list includes 157 full length cDNAs. In addition, 51 transcripts were characterized as spleen specific genes. The 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. This study provides deep-sequence data of rainbow trout's spleen transcriptome and identifies many new immune-related genes and full-length cDNAs. This data will help in identification of allelic variations suitable for applications of genomic selection and genetic manipulations in aquaculture.