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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Published in:BMC Genomics
Main Authors: Lukacs, Morten F, Harstad, Håvard, Bakke, Hege G, Beetz-Sargent, Marianne, McKinnel, Linda, Lubieniecki, Krzysztof P, Koop, Ben F, Grimholt, Unni
Format: Article in Journal/Newspaper
Language:English
Published: Springer Science and Business Media LLC 2010
Subjects:
Ula
Online Access:http://dx.doi.org/10.1186/1471-2164-11-154
https://link.springer.com/content/pdf/10.1186/1471-2164-11-154.pdf
id crspringernat:10.1186/1471-2164-11-154
record_format openpolar
spelling crspringernat:10.1186/1471-2164-11-154 2023-05-15T15:30:54+02:00 Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon Lukacs, Morten F Harstad, Håvard Bakke, Hege G Beetz-Sargent, Marianne McKinnel, Linda Lubieniecki, Krzysztof P Koop, Ben F Grimholt, Unni 2010 http://dx.doi.org/10.1186/1471-2164-11-154 https://link.springer.com/content/pdf/10.1186/1471-2164-11-154.pdf en eng Springer Science and Business Media LLC BMC Genomics volume 11, issue 1 ISSN 1471-2164 Genetics Biotechnology journal-article 2010 crspringernat https://doi.org/10.1186/1471-2164-11-154 2022-01-04T16:16:57Z 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 Springer Nature (via Crossref) Ula ENVELOPE(-57.139,-57.139,-64.086,-64.086) BMC Genomics 11 1 154
institution Open Polar
collection Springer Nature (via Crossref)
op_collection_id crspringernat
language English
topic Genetics
Biotechnology
spellingShingle Genetics
Biotechnology
Lukacs, Morten F
Harstad, Håvard
Bakke, Hege G
Beetz-Sargent, Marianne
McKinnel, Linda
Lubieniecki, Krzysztof P
Koop, Ben F
Grimholt, Unni
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
topic_facet Genetics
Biotechnology
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 Lukacs, Morten F
Harstad, Håvard
Bakke, Hege G
Beetz-Sargent, Marianne
McKinnel, Linda
Lubieniecki, Krzysztof P
Koop, Ben F
Grimholt, Unni
author_facet Lukacs, Morten F
Harstad, Håvard
Bakke, Hege G
Beetz-Sargent, Marianne
McKinnel, Linda
Lubieniecki, Krzysztof P
Koop, Ben F
Grimholt, Unni
author_sort Lukacs, Morten F
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 Springer Science and Business Media LLC
publishDate 2010
url http://dx.doi.org/10.1186/1471-2164-11-154
https://link.springer.com/content/pdf/10.1186/1471-2164-11-154.pdf
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
volume 11, issue 1
ISSN 1471-2164
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
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