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Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence
Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We iden...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971588/ https://www.ncbi.nlm.nih.gov/pubmed/24558256 http://dx.doi.org/10.1093/gbe/evu037 |
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author | Renny-Byfield, Simon Gallagher, Joseph P. Grover, Corrinne E. Szadkowski, Emmanuel Page, Justin T. Udall, Joshua A. Wang, Xiyin Paterson, Andrew H. Wendel, Jonathan F. |
author_facet | Renny-Byfield, Simon Gallagher, Joseph P. Grover, Corrinne E. Szadkowski, Emmanuel Page, Justin T. Udall, Joshua A. Wang, Xiyin Paterson, Andrew H. Wendel, Jonathan F. |
author_sort | Renny-Byfield, Simon |
collection | PubMed |
description | Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼60 Ma. |
format | Online Article Text |
id | pubmed-3971588 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-39715882014-04-01 Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence Renny-Byfield, Simon Gallagher, Joseph P. Grover, Corrinne E. Szadkowski, Emmanuel Page, Justin T. Udall, Joshua A. Wang, Xiyin Paterson, Andrew H. Wendel, Jonathan F. Genome Biol Evol Research Article Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼60 Ma. Oxford University Press 2014-02-19 /pmc/articles/PMC3971588/ /pubmed/24558256 http://dx.doi.org/10.1093/gbe/evu037 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Renny-Byfield, Simon Gallagher, Joseph P. Grover, Corrinne E. Szadkowski, Emmanuel Page, Justin T. Udall, Joshua A. Wang, Xiyin Paterson, Andrew H. Wendel, Jonathan F. Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence |
title | Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence |
title_full | Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence |
title_fullStr | Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence |
title_full_unstemmed | Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence |
title_short | Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence |
title_sort | ancient gene duplicates in gossypium (cotton) exhibit near-complete expression divergence |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971588/ https://www.ncbi.nlm.nih.gov/pubmed/24558256 http://dx.doi.org/10.1093/gbe/evu037 |
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