Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters
Hox cluster organization represents a valuable marker to study the effects of recent genome duplication in salmonid fish (25-100 million years ago). Using PCR amplification of cDNAs, BAC library screening and genome walking, we reconstructed 13 Hox clusters in the Atlantic salmon containing 118 Hox...
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fthighwire:oai:open-archive.highwire.org:molbiolevol:msn097v1 2023-05-15T15:31:23+02:00 Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters Mungpakdee, Sutada Seo, Hee-Chan Angotzi, Anna Rita Dong, Xianjun Akalin, Altuna Chourrout, Daniel 2008-04-18 20:43:34.0 text/html http://mbe.oxfordjournals.org/cgi/content/short/msn097v1 https://doi.org/10.1093/molbev/msn097 en eng Oxford University Press http://mbe.oxfordjournals.org/cgi/content/short/msn097v1 http://dx.doi.org/10.1093/molbev/msn097 Copyright (C) 2008, Society for Molecular Biology and Evolution Research Article TEXT 2008 fthighwire https://doi.org/10.1093/molbev/msn097 2013-05-27T15:56:02Z Hox cluster organization represents a valuable marker to study the effects of recent genome duplication in salmonid fish (25-100 million years ago). Using PCR amplification of cDNAs, BAC library screening and genome walking, we reconstructed 13 Hox clusters in the Atlantic salmon containing 118 Hox genes including 8 pseudogenes. Hox paralogs resulting from the genome duplication preceding the radiation of ray-finned fish have been much better preserved in salmon than in other model teleosts. The last genome duplication in the salmon lineage has been followed by the loss of one of the four HoxA clusters. Four rounds of genome duplication after the vertebrate ancestor, salmon Hox clusters display the main organizational features of vertebrate Hox clusters, with Hox genes exclusively that are densely packed in the same orientation. Recently duplicated Hox clusters have engaged a process of divergence, with several cases of pseudogenization or asymmetrical evolution of Hox gene duplicates, and a marked erosion of identity in non-coding sequences. Strikingly, the level of divergence attained strongly depends on the Hox cluster pairs, rather than on the Hox genes within each cluster. It is particularly high between both HoxBb clusters and both HoxDa clusters, while both HoxBa clusters remained virtually identical. Positive selection on the Hox protein coding sequences could not be detected. Text Atlantic salmon HighWire Press (Stanford University) Molecular Biology and Evolution 25 7 1333 1343 |
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Research Article |
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Research Article Mungpakdee, Sutada Seo, Hee-Chan Angotzi, Anna Rita Dong, Xianjun Akalin, Altuna Chourrout, Daniel Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters |
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Research Article |
description |
Hox cluster organization represents a valuable marker to study the effects of recent genome duplication in salmonid fish (25-100 million years ago). Using PCR amplification of cDNAs, BAC library screening and genome walking, we reconstructed 13 Hox clusters in the Atlantic salmon containing 118 Hox genes including 8 pseudogenes. Hox paralogs resulting from the genome duplication preceding the radiation of ray-finned fish have been much better preserved in salmon than in other model teleosts. The last genome duplication in the salmon lineage has been followed by the loss of one of the four HoxA clusters. Four rounds of genome duplication after the vertebrate ancestor, salmon Hox clusters display the main organizational features of vertebrate Hox clusters, with Hox genes exclusively that are densely packed in the same orientation. Recently duplicated Hox clusters have engaged a process of divergence, with several cases of pseudogenization or asymmetrical evolution of Hox gene duplicates, and a marked erosion of identity in non-coding sequences. Strikingly, the level of divergence attained strongly depends on the Hox cluster pairs, rather than on the Hox genes within each cluster. It is particularly high between both HoxBb clusters and both HoxDa clusters, while both HoxBa clusters remained virtually identical. Positive selection on the Hox protein coding sequences could not be detected. |
format |
Text |
author |
Mungpakdee, Sutada Seo, Hee-Chan Angotzi, Anna Rita Dong, Xianjun Akalin, Altuna Chourrout, Daniel |
author_facet |
Mungpakdee, Sutada Seo, Hee-Chan Angotzi, Anna Rita Dong, Xianjun Akalin, Altuna Chourrout, Daniel |
author_sort |
Mungpakdee, Sutada |
title |
Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters |
title_short |
Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters |
title_full |
Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters |
title_fullStr |
Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters |
title_full_unstemmed |
Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters |
title_sort |
differential evolution of the thirteen atlantic salmon hox clusters |
publisher |
Oxford University Press |
publishDate |
2008 |
url |
http://mbe.oxfordjournals.org/cgi/content/short/msn097v1 https://doi.org/10.1093/molbev/msn097 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://mbe.oxfordjournals.org/cgi/content/short/msn097v1 http://dx.doi.org/10.1093/molbev/msn097 |
op_rights |
Copyright (C) 2008, Society for Molecular Biology and Evolution |
op_doi |
https://doi.org/10.1093/molbev/msn097 |
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Molecular Biology and Evolution |
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25 |
container_issue |
7 |
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1333 |
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1343 |
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1766361876534394880 |