Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
Abstract Background We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA . A pseudolocus for Sasa-UCA was identified in...
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ftdoajarticles:oai:doaj.org/article:edcf7331ebb04ebcaf7493c5061718cc 2023-05-15T15:30:54+02:00 Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon Lubieniecki Krzysztof P McKinnel Linda Beetz-Sargent Marianne Bakke Hege G Harstad Håvard Lukacs Morten F Koop Ben F Grimholt Unni 2010-03-01T00:00:00Z https://doi.org/10.1186/1471-2164-11-154 https://doaj.org/article/edcf7331ebb04ebcaf7493c5061718cc EN eng BMC http://www.biomedcentral.com/1471-2164/11/154 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-11-154 1471-2164 https://doaj.org/article/edcf7331ebb04ebcaf7493c5061718cc BMC Genomics, Vol 11, Iss 1, p 154 (2010) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2010 ftdoajarticles https://doi.org/10.1186/1471-2164-11-154 2022-12-31T08:33:56Z Abstract Background We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA . A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region. Results The genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs were sequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IA region with 150 kb identifying the location of one Z-lineage locus, ZAA . The IB region was extended with 350 kb including three new Z-lineage loci, ZBA , ZCA and ZDA in addition to a UGA locus. An allelic version of the IB region contained a functional UDA locus in addition to the UCA pseudolocus. Additionally a BAC harbouring two MHC class I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus SAA (previously known as UAA ) was placed on LG10. Gene expression studies showed limited expression range for all class I genes with exception of UBA being dominantly expressed in gut, spleen and gills, and ZAA with high expression in blood. Conclusion Here we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages in Atlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IB regions, while three class I genes are found on two separate linkage groups. The gene organization of the two regions indicates that the IB region is evolving at a different pace than the IA region. Expression profiling, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one MHC class Ia gene ( UBA ), in addition to a multitude of nonclassical MHC class I genes from the U-, S- and Z-lineages. Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles Ula ENVELOPE(-57.139,-57.139,-64.086,-64.086) BMC Genomics 11 1 154 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Biotechnology TP248.13-248.65 Genetics QH426-470 Lubieniecki Krzysztof P McKinnel Linda Beetz-Sargent Marianne Bakke Hege G Harstad Håvard Lukacs Morten F Koop Ben F Grimholt Unni Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA . A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region. Results The genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs were sequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IA region with 150 kb identifying the location of one Z-lineage locus, ZAA . The IB region was extended with 350 kb including three new Z-lineage loci, ZBA , ZCA and ZDA in addition to a UGA locus. An allelic version of the IB region contained a functional UDA locus in addition to the UCA pseudolocus. Additionally a BAC harbouring two MHC class I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus SAA (previously known as UAA ) was placed on LG10. Gene expression studies showed limited expression range for all class I genes with exception of UBA being dominantly expressed in gut, spleen and gills, and ZAA with high expression in blood. Conclusion Here we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages in Atlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IB regions, while three class I genes are found on two separate linkage groups. The gene organization of the two regions indicates that the IB region is evolving at a different pace than the IA region. Expression profiling, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one MHC class Ia gene ( UBA ), in addition to a multitude of nonclassical MHC class I genes from the U-, S- and Z-lineages. |
format |
Article in Journal/Newspaper |
author |
Lubieniecki Krzysztof P McKinnel Linda Beetz-Sargent Marianne Bakke Hege G Harstad Håvard Lukacs Morten F Koop Ben F Grimholt Unni |
author_facet |
Lubieniecki Krzysztof P McKinnel Linda Beetz-Sargent Marianne Bakke Hege G Harstad Håvard Lukacs Morten F Koop Ben F Grimholt Unni |
author_sort |
Lubieniecki Krzysztof P |
title |
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon |
title_short |
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon |
title_full |
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon |
title_fullStr |
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon |
title_full_unstemmed |
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon |
title_sort |
comprehensive analysis of mhc class i genes from the u-, s-, and z-lineages in atlantic salmon |
publisher |
BMC |
publishDate |
2010 |
url |
https://doi.org/10.1186/1471-2164-11-154 https://doaj.org/article/edcf7331ebb04ebcaf7493c5061718cc |
long_lat |
ENVELOPE(-57.139,-57.139,-64.086,-64.086) |
geographic |
Ula |
geographic_facet |
Ula |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
BMC Genomics, Vol 11, Iss 1, p 154 (2010) |
op_relation |
http://www.biomedcentral.com/1471-2164/11/154 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-11-154 1471-2164 https://doaj.org/article/edcf7331ebb04ebcaf7493c5061718cc |
op_doi |
https://doi.org/10.1186/1471-2164-11-154 |
container_title |
BMC Genomics |
container_volume |
11 |
container_issue |
1 |
container_start_page |
154 |
_version_ |
1766361366568894464 |