Genomic Organisation Analysis of Novel Immunoglobulin-like Transcripts in Atlantic Salmon (Salmo salar) Reveals a Tightly Clustered and Multigene Family

Background: Several novel immunoglobulin-like transcripts (NILTs) which have previously been identified in thesalmonid species rainbow trout (Oncorhynchus mykiss) contain either one or two extracellular Ig domains of theV-type. NILTs also possess either an immunoreceptor tyrosine-based activating motif (ITAM) or immunoreceptortyrosine-based inhibitory motifs (ITIMs) in the cytoplasmic region resulting in different signalling abilities. Here wereport for the first time the genomic organisation and structure of the multigene family of NILTs in Atlantic salmon(Salmo salar) using a BAC sequencing approach.Results: We have identified six novel Atlantic salmon NILT genes (Ssa-NILT1-6), two pseudogenes (Ssa-NILTp1 andSsa-NILTp2) and seven genes encoding putative transposable elements in one BAC covering more than 200 kbp.Ssa-NILT1, 2, 4, 5 and 6 contain one Ig domain, all having a CX3C motif, whereas Ssa-NILT3 contains two Igdomains, having a CX6C motif in Ig1 and a CX7C motif in Ig2. Atlantic salmon NILTs possess several ITIMs in thecytoplasmic region and the ITIM-bearing exons are in phase 0. A comparison of identity between the amino acidsequences of the CX3C Ig domains from NILTs varies from 77% to 96%. Ssa-NILT1, 2, 3 and 4 were all confirmed tobe expressed either by their presence in EST databases (Ssa-NILT1) or RT-PCR (Ssa-NILT2, 3, and 4) using cDNA astemplate. A survey of the repertoire of putative NILT genes in a single individual revealed three novel genes (Ssa-NILT7-9) represented by the Ig domain, which together with Ig domains from Ssa-NILT1-6 could be divided intodifferent groups based on specific motifs.Conclusions: This report reveals a tightly clustered, multigene NILT family in Atlantic salmon. By screening a highlyredundant Atlantic salmon BAC library we have identified and characterised the genomic organisation of six genesencoding NILT receptors. The genes show similar characteristics to NILTs previously identified in rainbow trout,having highly conserved cysteines in the Ig domain and several inhibitory signalling motifs in the cytoplasmicregion. In a single individual three unique NILT Ig domain sequences were discovered at the genomic DNA level,which were divided into two different groups based on a four residue motif after the third cysteine. Our resultsfrom the BAC screening and analysis on the repertoire of NILT genes in a single individual indicates that manygenes of this expanding Ig containing NILT family are still to be discovered in fish.