Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon ( Salmo salar ) reveals a tightly clustered and multigene family
Abstract Background Several novel immunoglobulin-like transcripts (NILTs) which have previously been identified in the salmonid species rainbow trout ( Oncorhynchus mykiss ) contain either one or two extracellular Ig domains of the V-type. NILTs also possess either an immunoreceptor tyrosine-based a...
| Published in: | BMC Genomics |
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| Main Authors: | , , , , , |
| Format: | Article in Journal/Newspaper |
| Language: | English |
| Published: |
BMC
2010
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| Subjects: | |
| Online Access: | https://doi.org/10.1186/1471-2164-11-697 https://doaj.org/article/9373a90e6aa94a14ac39d0c862f01c14 |
| Summary: | Abstract Background Several novel immunoglobulin-like transcripts (NILTs) which have previously been identified in the salmonid species rainbow trout ( Oncorhynchus mykiss ) contain either one or two extracellular Ig domains of the V-type. NILTs also possess either an immunoreceptor tyrosine-based activating motif (ITAM) or immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in the cytoplasmic region resulting in different signalling abilities. Here we report 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 and Ssa-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 CX 3 C motif, whereas Ssa -NILT3 contains two Ig domains, having a CX 6 C motif in Ig1 and a CX 7 C motif in Ig2. Atlantic salmon NILTs possess several ITIMs in the cytoplasmic region and the ITIM-bearing exons are in phase 0. A comparison of identity between the amino acid sequences of the CX 3 C Ig domains from NILTs varies from 77% to 96%. Ssa-NILT1 , 2 , 3 and 4 were all confirmed to be expressed either by their presence in EST databases ( Ssa-NILT1 ) or RT-PCR ( Ssa-NILT2 , 3 , and 4 ) using cDNA as template. 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 into different groups based on specific motifs. Conclusions This report reveals a tightly clustered, multigene NILT family in Atlantic salmon. By screening a highly redundant Atlantic salmon BAC library we have identified and characterised the genomic organisation of six genes encoding NILT receptors. The genes show similar characteristics to NILTs previously identified in rainbow trout, having highly ... |
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