Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire
Abstract Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary process...
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ftdoajarticles:oai:doaj.org/article:0d6d7bc88c6b47f3b33bb972134c5f9e 2023-05-15T15:29:01+02:00 Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire Phillips Ruth B Davidson Evelyn A Chow William Lubieniecki Krzysztof P Boroevich Keith A Quinn Nicole L Koop Ben F Davidson William S 2010-10-01T00:00:00Z https://doi.org/10.1186/1471-2164-11-539 https://doaj.org/article/0d6d7bc88c6b47f3b33bb972134c5f9e EN eng BMC http://www.biomedcentral.com/1471-2164/11/539 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-11-539 1471-2164 https://doaj.org/article/0d6d7bc88c6b47f3b33bb972134c5f9e BMC Genomics, Vol 11, Iss 1, p 539 (2010) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2010 ftdoajarticles https://doi.org/10.1186/1471-2164-11-539 2022-12-31T07:10:01Z Abstract Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves the loss of a single hemoglobin gene cluster ... Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles BMC Genomics 11 1 |
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Directory of Open Access Journals: DOAJ Articles |
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Biotechnology TP248.13-248.65 Genetics QH426-470 |
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Biotechnology TP248.13-248.65 Genetics QH426-470 Phillips Ruth B Davidson Evelyn A Chow William Lubieniecki Krzysztof P Boroevich Keith A Quinn Nicole L Koop Ben F Davidson William S Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves the loss of a single hemoglobin gene cluster ... |
format |
Article in Journal/Newspaper |
author |
Phillips Ruth B Davidson Evelyn A Chow William Lubieniecki Krzysztof P Boroevich Keith A Quinn Nicole L Koop Ben F Davidson William S |
author_facet |
Phillips Ruth B Davidson Evelyn A Chow William Lubieniecki Krzysztof P Boroevich Keith A Quinn Nicole L Koop Ben F Davidson William S |
author_sort |
Phillips Ruth B |
title |
Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire |
title_short |
Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire |
title_full |
Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire |
title_fullStr |
Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire |
title_full_unstemmed |
Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire |
title_sort |
genomic organization and evolution of the atlantic salmon hemoglobin repertoire |
publisher |
BMC |
publishDate |
2010 |
url |
https://doi.org/10.1186/1471-2164-11-539 https://doaj.org/article/0d6d7bc88c6b47f3b33bb972134c5f9e |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
BMC Genomics, Vol 11, Iss 1, p 539 (2010) |
op_relation |
http://www.biomedcentral.com/1471-2164/11/539 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-11-539 1471-2164 https://doaj.org/article/0d6d7bc88c6b47f3b33bb972134c5f9e |
op_doi |
https://doi.org/10.1186/1471-2164-11-539 |
container_title |
BMC Genomics |
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11 |
container_issue |
1 |
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1766359396199170048 |