Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence...
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ftpubmed:oai:pubmedcentral.nih.gov:4573066 2023-05-15T17:54:16+02:00 Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster Gao, Dahai Ko, Dennis C. Tian, Xinmin Yang, Guang Wang, Liuyang 2015-09-13 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573066/ http://www.ncbi.nlm.nih.gov/pubmed/26417197 https://doi.org/10.4137/EBO.S30230 en eng Libertas Academica http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573066/ http://www.ncbi.nlm.nih.gov/pubmed/26417197 http://dx.doi.org/10.4137/EBO.S30230 © 2015 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License. CC-BY-NC Original Research Text 2015 ftpubmed https://doi.org/10.4137/EBO.S30230 2015-10-04T00:23:52Z Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence and the functional maintenance of duplicate genes remain little understood. In the present study, we performed a comprehensive analysis of duplicate genes in the protein kinase superfamily using whole genome and transcriptome data for the Pacific oyster. A total of 64 duplicated gene pairs were identified based on a phylogenetic approach and the reciprocal best BLAST method. By analyzing gene expression from RNA-seq data from 69 different developmental and stimuli-induced conditions (nine tissues, 38 developmental stages, eight dry treatments, seven heat treatments, and seven salty treatments), we found that expression patterns were significantly correlated for a number of duplicate gene pairs, suggesting the conservation of regulatory mechanisms following divergence. Our analysis also identified a subset of duplicate gene pairs with very high expression divergence, indicating that these gene pairs may have been subjected to transcriptional subfunctionalization or neofunctionalization after the initial duplication events. Further analysis revealed a significant correlation between expression and sequence divergence (as revealed by synonymous or nonsynonymous substitution rates) under certain conditions. Taken together, these results provide evidence for duplicate gene sequence and expression divergence in the Pacific oyster, accompanying its adaptation to harsh environments. Our results provide new insights into the evolution of duplicate genes and their expression levels in the Pacific oyster. Text Pacific oyster PubMed Central (PMC) Pacific Evolutionary Bioinformatics 11s1 EBO.S30230 |
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Original Research Gao, Dahai Ko, Dennis C. Tian, Xinmin Yang, Guang Wang, Liuyang Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster |
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Original Research |
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Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence and the functional maintenance of duplicate genes remain little understood. In the present study, we performed a comprehensive analysis of duplicate genes in the protein kinase superfamily using whole genome and transcriptome data for the Pacific oyster. A total of 64 duplicated gene pairs were identified based on a phylogenetic approach and the reciprocal best BLAST method. By analyzing gene expression from RNA-seq data from 69 different developmental and stimuli-induced conditions (nine tissues, 38 developmental stages, eight dry treatments, seven heat treatments, and seven salty treatments), we found that expression patterns were significantly correlated for a number of duplicate gene pairs, suggesting the conservation of regulatory mechanisms following divergence. Our analysis also identified a subset of duplicate gene pairs with very high expression divergence, indicating that these gene pairs may have been subjected to transcriptional subfunctionalization or neofunctionalization after the initial duplication events. Further analysis revealed a significant correlation between expression and sequence divergence (as revealed by synonymous or nonsynonymous substitution rates) under certain conditions. Taken together, these results provide evidence for duplicate gene sequence and expression divergence in the Pacific oyster, accompanying its adaptation to harsh environments. Our results provide new insights into the evolution of duplicate genes and their expression levels in the Pacific oyster. |
format |
Text |
author |
Gao, Dahai Ko, Dennis C. Tian, Xinmin Yang, Guang Wang, Liuyang |
author_facet |
Gao, Dahai Ko, Dennis C. Tian, Xinmin Yang, Guang Wang, Liuyang |
author_sort |
Gao, Dahai |
title |
Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster |
title_short |
Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster |
title_full |
Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster |
title_fullStr |
Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster |
title_full_unstemmed |
Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster |
title_sort |
expression divergence of duplicate genes in the protein kinase superfamily in pacific oyster |
publisher |
Libertas Academica |
publishDate |
2015 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573066/ http://www.ncbi.nlm.nih.gov/pubmed/26417197 https://doi.org/10.4137/EBO.S30230 |
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Pacific |
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Pacific |
genre |
Pacific oyster |
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Pacific oyster |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573066/ http://www.ncbi.nlm.nih.gov/pubmed/26417197 http://dx.doi.org/10.4137/EBO.S30230 |
op_rights |
© 2015 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License. |
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CC-BY-NC |
op_doi |
https://doi.org/10.4137/EBO.S30230 |
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Evolutionary Bioinformatics |
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11s1 |
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EBO.S30230 |
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1766162012279144448 |