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 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...
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ftunivwagenin:oai:library.wur.nl:wurpubs/408226 2024-02-04T09:58:52+01:00 Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family Ostergaard, A.E. Lubieniecki, K.P. Martin, S.A.M. Stet, R.J.M. Davidson, W.S. Secombes, C.J. 2010 application/pdf https://research.wur.nl/en/publications/genomic-organisation-analysis-of-novel-immunoglobulin-like-transc https://doi.org/10.1186/1471-2164-11-697 en eng https://edepot.wur.nl/175428 https://research.wur.nl/en/publications/genomic-organisation-analysis-of-novel-immunoglobulin-like-transc doi:10.1186/1471-2164-11-697 info:eu-repo/semantics/openAccess Wageningen University & Research BMC Genomics 11 (2010) ISSN: 1471-2164 complex cutting edge genes immune-type receptor inhibitory receptors natural-killer-cells nkp44 oncorhynchus-mykiss rainbow-trout sequence alignment info:eu-repo/semantics/article Article/Letter to editor info:eu-repo/semantics/publishedVersion 2010 ftunivwagenin https://doi.org/10.1186/1471-2164-11-697 2024-01-10T23:22:46Z 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 CX3C motif, whereas Ssa-NILT3 contains two Ig domains, having a CX6C motif in Ig1 and a CX7C 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 CX3C 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 conserved cysteines in the Ig ... Article in Journal/Newspaper Atlantic salmon Salmo salar Wageningen UR (University & Research Centre): Digital Library BMC Genomics 11 1 |
institution |
Open Polar |
collection |
Wageningen UR (University & Research Centre): Digital Library |
op_collection_id |
ftunivwagenin |
language |
English |
topic |
complex cutting edge genes immune-type receptor inhibitory receptors natural-killer-cells nkp44 oncorhynchus-mykiss rainbow-trout sequence alignment |
spellingShingle |
complex cutting edge genes immune-type receptor inhibitory receptors natural-killer-cells nkp44 oncorhynchus-mykiss rainbow-trout sequence alignment Ostergaard, A.E. Lubieniecki, K.P. Martin, S.A.M. Stet, R.J.M. Davidson, W.S. Secombes, C.J. Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family |
topic_facet |
complex cutting edge genes immune-type receptor inhibitory receptors natural-killer-cells nkp44 oncorhynchus-mykiss rainbow-trout sequence alignment |
description |
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 CX3C motif, whereas Ssa-NILT3 contains two Ig domains, having a CX6C motif in Ig1 and a CX7C 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 CX3C 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 conserved cysteines in the Ig ... |
format |
Article in Journal/Newspaper |
author |
Ostergaard, A.E. Lubieniecki, K.P. Martin, S.A.M. Stet, R.J.M. Davidson, W.S. Secombes, C.J. |
author_facet |
Ostergaard, A.E. Lubieniecki, K.P. Martin, S.A.M. Stet, R.J.M. Davidson, W.S. Secombes, C.J. |
author_sort |
Ostergaard, A.E. |
title |
Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family |
title_short |
Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family |
title_full |
Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family |
title_fullStr |
Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family |
title_full_unstemmed |
Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family |
title_sort |
genomic organisation analysis of novel immunoglobulin-like transcripts in atlantic salmon (salmo salar) reveals a tightly clustered and multigene family |
publishDate |
2010 |
url |
https://research.wur.nl/en/publications/genomic-organisation-analysis-of-novel-immunoglobulin-like-transc https://doi.org/10.1186/1471-2164-11-697 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
BMC Genomics 11 (2010) ISSN: 1471-2164 |
op_relation |
https://edepot.wur.nl/175428 https://research.wur.nl/en/publications/genomic-organisation-analysis-of-novel-immunoglobulin-like-transc doi:10.1186/1471-2164-11-697 |
op_rights |
info:eu-repo/semantics/openAccess Wageningen University & Research |
op_doi |
https://doi.org/10.1186/1471-2164-11-697 |
container_title |
BMC Genomics |
container_volume |
11 |
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1 |
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1789963445474426880 |