Differential expression and evolution of three tandem, interleukin-1 receptor-like 1 genes in rainbow trout (Oncorhynchus mykiss)

Authors: Shaw, Cassidy; Gao, Guangtu; Wiens, Gregory - Greg

Submitted to: Developmental and Comparative Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/6/2018
Publication Date: 6/15/2018
Citation: Shaw, C.H., Gao, G., Wiens, G.D. 2018. Differential expression and evolution of three tandem, interleukin-1 receptor-like 1 genes in rainbow trout (Oncorhynchus mykiss). Developmental and Comparative Immunology. 87:193-203. https://doi.org/10.1016/j.dci.2018.06.003.
DOI: https://doi.org/10.1016/j.dci.2018.06.003

Interpretive Summary: Bacterial cold water disease (BCWD) is a frequent source of mortality in rainbow trout aquaculture. Selective breeding has been used to produce a resistant line of rainbow trout that demonstrate increased survival following experimental and natural exposure to BCWD. As part of an effort to determine the mechanisms behind rainbow trout resistance to BCWD, we have identified for the first time, three interleukin-1 receptor like-1 (il1rl1) genes within a genetic locus associated with disease resistance. Here, we describe the structure of these genes, their expression in rainbow trout tissues and their phylogenetic relationship to similar genes in mammals, birds and other fish species. The genes are 95% similar to one another and also appear in other salmonid species including Atlantic salmon and Coho salmon. All three trout il1rl1 genes are expressed throughout the body and one of the copies is expressed at significantly higher levels than the other two copies in all tissues tested. One gene copy in both Atlantic salmon and coho salmon appears to be nonfunctional. These findings increase our knowledge of fish immune genes and further their potential contribution to disease resistance.

Technical Abstract: Interleukin-1 receptor-like 1 (Il1rl1 or ST2), a member of the Interleukin-1 Receptor family, has pleiotropic roles including tissue homeostasis, inflammation, immune polarization, and disease resistance in mammals. A single orthologue was previously described in salmonid fish; however, a recently improved genome assembly of rainbow trout (Oncorhynchus mykiss) revealed three adjacent, tandem il1rl1 orthologues on chromosome Omy 03. Here, we report the genomic organization and evolution of the three il1rl1 genes (il1rl1 genes 1-3), and use both RNA-seq and gene-specific qPCR methods to quantify expression patterns. Nucleotide sequence homology between the three genes is >95% and each predicted protein contains three IG/IG-like domains, a transmembrane region and a TIR domain. The amino acid sequence homology of the rainbow trout il1rl1 genes are highly related to Atlantic and Coho salmon (~94%) but relatively low (22-26%) with avian and mammalian species. Analysis of transcript abundance in 15 tissues obtained from healthy adult rainbow trout by RNA-seq indicates constitutive expression of all three genes with the highest relative expression of gene-1 in oocyte tissue and highest expression of gene-2 and -3 in gill tissue. qPCR assays specific to Il1rl1 gene-1 or -3, as well as a multi-gene qPCR assay (combined genes 1-3), confirmed that gene-1 is >20 fold more highly expressed than genes-2 and -3 in whole body lysates. Unrooted phylogenetic trees grouped the il1rl1 genes apart from other genes of the interleukin 1 receptor family and genomic comparisons identify preserved synteny between mammals, birds and salmonids albeit a pseudogene is present in both Atlantic salmon and Coho salmon. Phylogenetic analyses suggest these genes arose by tandem duplication but are inconclusive whether these events occurred prior-to or after speciation. These findings further the understanding of interleukin receptor family evolution and their contribution to teleost immune function.