Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar )
Abstract Background We have previously identified associations between major histocompatibility complex (MHC) class I and resistance towards bacterial and viral pathogens in Atlantic salmon. To evaluate if only MHC or also closely linked genes contributed to the observed resistance we ventured into...
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ftdoajarticles:oai:doaj.org/article:2dcbd7883dc24cc3b008ee9f150c31aa 2023-05-15T15:28:32+02:00 Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar ) Phillips Ruth B Bakke Hege G Reid Linda Cooper Glenn A Beetz-Sargent Marianne Grimholt Unni Harstad Håvard Lukacs Morten F Miller Kristina M Davidson William S Koop Ben F 2007-07-01T00:00:00Z https://doi.org/10.1186/1471-2164-8-251 https://doaj.org/article/2dcbd7883dc24cc3b008ee9f150c31aa EN eng BMC http://www.biomedcentral.com/1471-2164/8/251 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-8-251 1471-2164 https://doaj.org/article/2dcbd7883dc24cc3b008ee9f150c31aa BMC Genomics, Vol 8, Iss 1, p 251 (2007) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2007 ftdoajarticles https://doi.org/10.1186/1471-2164-8-251 2022-12-31T08:35:27Z Abstract Background We have previously identified associations between major histocompatibility complex (MHC) class I and resistance towards bacterial and viral pathogens in Atlantic salmon. To evaluate if only MHC or also closely linked genes contributed to the observed resistance we ventured into sequencing of the duplicated MHC class I regions of Atlantic salmon. Results Nine BACs covering more than 500 kb of the two duplicated MHC class I regions of Atlantic salmon were sequenced and the gene organizations characterized. Both regions contained the proteasome components PSMB8, PSMB9, PSMB9-like and PSMB10 in addition to the transporter for antigen processing TAP2, as well as genes for KIFC1, ZBTB22, DAXX, TAPBP, BRD2, COL11A2, RXRB and SLC39A7. The IA region contained the recently reported MHC class I Sasa-ULA locus residing approximately 50 kb upstream of the major Sasa-UBA locus. The duplicated class IB region contained an MHC class I locus resembling the rainbow trout UCA locus, but although transcribed it was a pseudogene. No other MHC class I-like genes were detected in the two duplicated regions. Two allelic BACs spanning the UBA locus had 99.2% identity over 125 kb, while the IA region showed 82.5% identity over 136 kb to the IB region. The Atlantic salmon IB region had an insert of 220 kb in comparison to the IA region containing three chitin synthase genes. Conclusion We have characterized the gene organization of more than 500 kb of the two duplicated MHC class I regions in Atlantic salmon. Although Atlantic salmon and rainbow trout are closely related, the gene organization of their IB region has undergone extensive gene rearrangements. The Atlantic salmon has only one class I UCA pseudogene in the IB region while trout contains the four MHC UCA , UDA , UEA and UFA class I loci. The large differences in gene content and most likely function of the salmon and trout class IB region clearly argues that sequencing of salmon will not necessarily provide information relevant for trout and vice versa. Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles Ula ENVELOPE(-57.139,-57.139,-64.086,-64.086) BMC Genomics 8 1 251 |
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 Phillips Ruth B Bakke Hege G Reid Linda Cooper Glenn A Beetz-Sargent Marianne Grimholt Unni Harstad Håvard Lukacs Morten F Miller Kristina M Davidson William S Koop Ben F Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar ) |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background We have previously identified associations between major histocompatibility complex (MHC) class I and resistance towards bacterial and viral pathogens in Atlantic salmon. To evaluate if only MHC or also closely linked genes contributed to the observed resistance we ventured into sequencing of the duplicated MHC class I regions of Atlantic salmon. Results Nine BACs covering more than 500 kb of the two duplicated MHC class I regions of Atlantic salmon were sequenced and the gene organizations characterized. Both regions contained the proteasome components PSMB8, PSMB9, PSMB9-like and PSMB10 in addition to the transporter for antigen processing TAP2, as well as genes for KIFC1, ZBTB22, DAXX, TAPBP, BRD2, COL11A2, RXRB and SLC39A7. The IA region contained the recently reported MHC class I Sasa-ULA locus residing approximately 50 kb upstream of the major Sasa-UBA locus. The duplicated class IB region contained an MHC class I locus resembling the rainbow trout UCA locus, but although transcribed it was a pseudogene. No other MHC class I-like genes were detected in the two duplicated regions. Two allelic BACs spanning the UBA locus had 99.2% identity over 125 kb, while the IA region showed 82.5% identity over 136 kb to the IB region. The Atlantic salmon IB region had an insert of 220 kb in comparison to the IA region containing three chitin synthase genes. Conclusion We have characterized the gene organization of more than 500 kb of the two duplicated MHC class I regions in Atlantic salmon. Although Atlantic salmon and rainbow trout are closely related, the gene organization of their IB region has undergone extensive gene rearrangements. The Atlantic salmon has only one class I UCA pseudogene in the IB region while trout contains the four MHC UCA , UDA , UEA and UFA class I loci. The large differences in gene content and most likely function of the salmon and trout class IB region clearly argues that sequencing of salmon will not necessarily provide information relevant for trout and vice versa. |
format |
Article in Journal/Newspaper |
author |
Phillips Ruth B Bakke Hege G Reid Linda Cooper Glenn A Beetz-Sargent Marianne Grimholt Unni Harstad Håvard Lukacs Morten F Miller Kristina M Davidson William S Koop Ben F |
author_facet |
Phillips Ruth B Bakke Hege G Reid Linda Cooper Glenn A Beetz-Sargent Marianne Grimholt Unni Harstad Håvard Lukacs Morten F Miller Kristina M Davidson William S Koop Ben F |
author_sort |
Phillips Ruth B |
title |
Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar ) |
title_short |
Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar ) |
title_full |
Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar ) |
title_fullStr |
Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar ) |
title_full_unstemmed |
Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar ) |
title_sort |
genomic organization of duplicated major histocompatibility complex class i regions in atlantic salmon ( salmo salar ) |
publisher |
BMC |
publishDate |
2007 |
url |
https://doi.org/10.1186/1471-2164-8-251 https://doaj.org/article/2dcbd7883dc24cc3b008ee9f150c31aa |
long_lat |
ENVELOPE(-57.139,-57.139,-64.086,-64.086) |
geographic |
Ula |
geographic_facet |
Ula |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
BMC Genomics, Vol 8, Iss 1, p 251 (2007) |
op_relation |
http://www.biomedcentral.com/1471-2164/8/251 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-8-251 1471-2164 https://doaj.org/article/2dcbd7883dc24cc3b008ee9f150c31aa |
op_doi |
https://doi.org/10.1186/1471-2164-8-251 |
container_title |
BMC Genomics |
container_volume |
8 |
container_issue |
1 |
container_start_page |
251 |
_version_ |
1766358880190726144 |