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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #300961
Title: Characterization of rainbow trout (Oncorhynchus mykiss) spleen transcriptome and identification of immune-related genes

Author
item ALI, ALI - Middle Tennessee State University
item ELMUSHARAF, REEM - Middle Tennessee State University
item Palti, Yniv
item Rexroad, Caird
item YAO, JIANBO - West Virginia University
item SALEM, MOHAMED - Middle Tennessee State University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/16/2013
Publication Date: 1/12/2014
Citation: Ali, A., Elmusharaf, R., Palti, Y., Rexroad III, C.E., Yao, J., Salem, M. 2014. Characterization of rainbow trout (Oncorhynchus mykiss) spleen transcriptome and identification of immune-related genes. Plant and Animal Genome Conference. 354.

Interpretive Summary:

Technical Abstract: Resistance against specific diseases is affecting profitability in fish production systems including rainbow trout. Limited information is known about functions and mechanisms of the immune gene pathways in teleosts. Immunogenomics are powerful tools to determine immune-related genes/gene pathways and develop genetic markers for genomic-assisted selection. 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 metabolic processes (17.60%), signaling (14.93%), response to stimuli (12.21%) and receptor activity (7.41%) and suggest existence of many immune-related proteins. KEGG annotation revealed 2,828 annotated sequences belonging to “organismal systems” with high number of sequences, 845 (29.88%), assigned to immune systems. A number of sequences, some annotated 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. Moreover, 52 transcripts were identified as spleen specific genes. 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 the rainbow trout's spleen transcriptome and identifies many new immune-related genes. These data are useful for identification of allelic variations suitable for applications in genomic-assisted selection and genetic manipulations.