Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome
BioMed Central Background: Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional...
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ftuvicpubl:oai:dspace.library.uvic.ca:1828/5531 2023-05-15T15:31:45+02:00 Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome Leong, Jong S. Jantzen, Stuart G. Von Schalburg, Kristian Robert Cooper, Glenn A. Messmer, Amber M. Liao, Nancy Y. Munro, Sarah Moore, Richard Holt, Robert A. Jones, Steven J.M. Davidson, William S. Koop, Benjamin F. 2010 application/pdf http://hdl.handle.net/1828/5531 http://www.biomedcentral.com/1471-2164/11/279 https://doi.org/10.1186/1471-2164-11-279 en eng BioMed Central Leong et al., Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome BMC Genomics 2010, 11:279 http://www.biomedcentral.com/1471-2164/11/279 http://dx.doi.org/10.1186/1471-2164-11-279 http://hdl.handle.net/1828/5531 Article 2010 ftuvicpubl https://doi.org/10.1186/1471-2164-11-279 2022-05-19T06:14:20Z BioMed Central Background: Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar), but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution. Results: From existing expressed sequence tag (EST) resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (Esox lucius) ESTs. Pairwise dN/dS comparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates. Conclusions: 9,057 full-length reference genes were characterized in S. salar and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate. This project was funded by Genome Canada and Genome BC. Faculty Reviewed Article in Journal/Newspaper Atlantic salmon Salmo salar University of Victoria (Canada): UVicDSpace Canada BMC Genomics 11 1 279 |
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University of Victoria (Canada): UVicDSpace |
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ftuvicpubl |
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English |
description |
BioMed Central Background: Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar), but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution. Results: From existing expressed sequence tag (EST) resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (Esox lucius) ESTs. Pairwise dN/dS comparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates. Conclusions: 9,057 full-length reference genes were characterized in S. salar and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate. This project was funded by Genome Canada and Genome BC. Faculty Reviewed |
format |
Article in Journal/Newspaper |
author |
Leong, Jong S. Jantzen, Stuart G. Von Schalburg, Kristian Robert Cooper, Glenn A. Messmer, Amber M. Liao, Nancy Y. Munro, Sarah Moore, Richard Holt, Robert A. Jones, Steven J.M. Davidson, William S. Koop, Benjamin F. |
spellingShingle |
Leong, Jong S. Jantzen, Stuart G. Von Schalburg, Kristian Robert Cooper, Glenn A. Messmer, Amber M. Liao, Nancy Y. Munro, Sarah Moore, Richard Holt, Robert A. Jones, Steven J.M. Davidson, William S. Koop, Benjamin F. Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome |
author_facet |
Leong, Jong S. Jantzen, Stuart G. Von Schalburg, Kristian Robert Cooper, Glenn A. Messmer, Amber M. Liao, Nancy Y. Munro, Sarah Moore, Richard Holt, Robert A. Jones, Steven J.M. Davidson, William S. Koop, Benjamin F. |
author_sort |
Leong, Jong S. |
title |
Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome |
title_short |
Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome |
title_full |
Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome |
title_fullStr |
Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome |
title_full_unstemmed |
Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome |
title_sort |
salmo salar and esox lucius full-length cdna sequences reveal changes in evolutionary pressures on a post-tetraploidization genome |
publisher |
BioMed Central |
publishDate |
2010 |
url |
http://hdl.handle.net/1828/5531 http://www.biomedcentral.com/1471-2164/11/279 https://doi.org/10.1186/1471-2164-11-279 |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
Leong et al., Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome BMC Genomics 2010, 11:279 http://www.biomedcentral.com/1471-2164/11/279 http://dx.doi.org/10.1186/1471-2164-11-279 http://hdl.handle.net/1828/5531 |
op_doi |
https://doi.org/10.1186/1471-2164-11-279 |
container_title |
BMC Genomics |
container_volume |
11 |
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1 |
container_start_page |
279 |
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1766362279500054528 |