title: 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.
authors.affiliation: Department of Biology, Middle Tennessee State University Murfreesboro, TN, USA ; Department of Zoology, Faculty of Science, Benha University Benha, Egypt.
authors.forename: Ali
authors.initials: A
authors.lastname: Ali
authors.affiliation: The National Center for Cool and Cold Water Aquaculture, United States Department of Agriculture Agricultural Research Service Leetown, WV USA.
authors.forename: Caird E
authors.initials: CE
authors.lastname: Rexroad
authors.affiliation: School of Biological Sciences, Washington State University Pullman, WA, USA.
authors.forename: Gary H
authors.initials: GH
authors.lastname: Thorgaard
authors.affiliation: Division of Animal and Nutritional Science, West Virginia University Morgantown, WV, USA.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Yao
authors.affiliation: Department of Biology, Middle Tennessee State University Murfreesboro, TN, USA ; Division of Animal and Nutritional Science, West Virginia University Morgantown, WV, USA.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Salem
keywords: KEGG; annotation; full-length cDNA; immune-related genes; spleen transcriptome; spleen-specific genes