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Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton
BACKGROUND: Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. The availability of the whole-genome data of different cotton species allows us...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604486/ https://www.ncbi.nlm.nih.gov/pubmed/31262248 http://dx.doi.org/10.1186/s12864-019-5928-2 |
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author | Li, Weixi Zhang, Dayong Zhu, Guozhong Mi, Xinyue Guo, Wangzhen |
author_facet | Li, Weixi Zhang, Dayong Zhu, Guozhong Mi, Xinyue Guo, Wangzhen |
author_sort | Li, Weixi |
collection | PubMed |
description | BACKGROUND: Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. The availability of the whole-genome data of different cotton species allows us to study systematic evolution and function of cotton AQPs on a genome-wide level. RESULTS: Here, a total of 53, 58, 113 and 111 AQP genes were identified in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. A comprehensive analysis of cotton AQPs, involved in exon/intron structure, functional domains, phylogenetic relationships and gene duplications, divided these AQPs into five subfamilies (PIP, NIP, SIP, TIP and XIP). Comparative genome analysis among 30 species from algae to angiosperm as well as common tandem duplication events in 24 well-studied plants further revealed the evolutionary conservation of AQP family in the organism kingdom. Combining transcriptome analysis and Quantitative Real-time PCR (qRT-PCR) verification, most AQPs exhibited tissue-specific expression patterns both in G. raimondii and G. hirsutum. Meanwhile, a bias of time to peak expression of several AQPs was also detected after treating G. davidsonii and G. hirsutum with 200 mM NaCl. It is interesting that both PIP1;4 h/i/j and PIP2;2a/e showed the highly conserved tandem structure, but differentially contributed to tissue development and stress response in different cotton species. CONCLUSIONS: These results demonstrated that cotton AQPs were structural conservation while experienced the functional differentiation during the process of evolution and domestication. This study will further broaden our insights into the evolution and functional elucidation of AQP gene family in cotton. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5928-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6604486 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-66044862019-07-12 Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton Li, Weixi Zhang, Dayong Zhu, Guozhong Mi, Xinyue Guo, Wangzhen BMC Genomics Research Article BACKGROUND: Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. The availability of the whole-genome data of different cotton species allows us to study systematic evolution and function of cotton AQPs on a genome-wide level. RESULTS: Here, a total of 53, 58, 113 and 111 AQP genes were identified in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. A comprehensive analysis of cotton AQPs, involved in exon/intron structure, functional domains, phylogenetic relationships and gene duplications, divided these AQPs into five subfamilies (PIP, NIP, SIP, TIP and XIP). Comparative genome analysis among 30 species from algae to angiosperm as well as common tandem duplication events in 24 well-studied plants further revealed the evolutionary conservation of AQP family in the organism kingdom. Combining transcriptome analysis and Quantitative Real-time PCR (qRT-PCR) verification, most AQPs exhibited tissue-specific expression patterns both in G. raimondii and G. hirsutum. Meanwhile, a bias of time to peak expression of several AQPs was also detected after treating G. davidsonii and G. hirsutum with 200 mM NaCl. It is interesting that both PIP1;4 h/i/j and PIP2;2a/e showed the highly conserved tandem structure, but differentially contributed to tissue development and stress response in different cotton species. CONCLUSIONS: These results demonstrated that cotton AQPs were structural conservation while experienced the functional differentiation during the process of evolution and domestication. This study will further broaden our insights into the evolution and functional elucidation of AQP gene family in cotton. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5928-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-07-01 /pmc/articles/PMC6604486/ /pubmed/31262248 http://dx.doi.org/10.1186/s12864-019-5928-2 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Li, Weixi Zhang, Dayong Zhu, Guozhong Mi, Xinyue Guo, Wangzhen Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton |
title | Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton |
title_full | Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton |
title_fullStr | Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton |
title_full_unstemmed | Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton |
title_short | Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton |
title_sort | combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604486/ https://www.ncbi.nlm.nih.gov/pubmed/31262248 http://dx.doi.org/10.1186/s12864-019-5928-2 |
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