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.
Highlights
Teleost fish are the first class of vertebrates that have the elements of both innate and adaptive immune responses (Whyte, 2007)
The spleen transcriptome was sequenced from an apparently healthy single homozygous doubled-haploid fish from the Swanson clonal line, the same line used for BAC library construction (Palti et al, 2004) and sequencing both of the whole transcriptome (Salem et al, 2010) and the whole genome reference (Berthelot et al, 2014)
A single doubled-haploid fish was used to help overcome the assembly complications associated with the tetraploid genome of the rainbow trout (Allendorf and Thorgaard, 1984)
Summary
Teleost fish are the first class of vertebrates that have the elements of both innate and adaptive immune responses (Whyte, 2007). Innate immunity is more important in teleosts as the first line of defense due to the restrictions on adaptive immunity in suboptimal environments (Ullal et al, 2008). Teleost fish have no bone marrow or lymph nodes. The ability of fish to combat viral, bacterial or parasitic pathogen is affected by genetic factors. Genetic selection can improve disease resistance and provide prolonged protection against pathogens (Skamene and Pietrangeli, 1991; Wiegertjes et al, 1996; Van Muiswinkel et al, 1999; Leeds et al, 2010; Wiens et al, 2013a). Investigations on immune reactions in fish could aid in development of vaccines (Raida and Buchmann, 2009)
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