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Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

BACKGROUND: Expansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). In this work, we performed a comprehensive stud...

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Autores principales: Han, Zhisheng, Liu, Yanlin, Deng, Xiong, Liu, Dongmiao, Liu, Yue, Hu, Yingkao, Yan, Yueming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359794/
https://www.ncbi.nlm.nih.gov/pubmed/30709338
http://dx.doi.org/10.1186/s12864-019-5455-1
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author Han, Zhisheng
Liu, Yanlin
Deng, Xiong
Liu, Dongmiao
Liu, Yue
Hu, Yingkao
Yan, Yueming
author_facet Han, Zhisheng
Liu, Yanlin
Deng, Xiong
Liu, Dongmiao
Liu, Yue
Hu, Yingkao
Yan, Yueming
author_sort Han, Zhisheng
collection PubMed
description BACKGROUND: Expansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). In this work, we performed a comprehensive study on the molecular characterization, phylogenetic relationship and expression profiling of common wheat (Triticum aestivum) expansin gene family using the recently released wheat genome database (IWGSC RefSeq v1.1 with a coverage rate of 94%). RESULTS: Genome-wide analysis identified 241 expansin genes in the wheat genome, which were grouped into three subfamilies (EXPA, EXPB and EXLA) by phylogenetic tree. Molecular structure analysis showed that wheat expansin gene family showed high evolutionary conservation although some differences were present in different subfamilies. Some key amino acid sites that contribute to functional divergence, positive selection, and coevolution were detected. Evolutionary analysis revealed that wheat expansin gene superfamily underwent strong positive selection. The transcriptome map and qRT-PCR analysis found that wheat expansin genes had tissue/organ expression specificity and preference, and generally highly expressed in the roots. The expression levels of some expansin genes were significantly induced by NaCl and polyethylene glycol stresses, which was consistent with the differential distribution of the cis-elements in the promoter region. CONCLUSIONS: Wheat expansin gene family showed high evolutionary conservation and wide range of functional divergence. Different selection constraints may influence the evolution of the three expansin subfamilies. The different expression patterns demonstrated that expansin genes could play important roles in plant growth and abiotic stress responses. This study provides new insights into the structures, evolution and functions of wheat expansin gene family. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5455-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-63597942019-02-07 Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.) Han, Zhisheng Liu, Yanlin Deng, Xiong Liu, Dongmiao Liu, Yue Hu, Yingkao Yan, Yueming BMC Genomics Research Article BACKGROUND: Expansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). In this work, we performed a comprehensive study on the molecular characterization, phylogenetic relationship and expression profiling of common wheat (Triticum aestivum) expansin gene family using the recently released wheat genome database (IWGSC RefSeq v1.1 with a coverage rate of 94%). RESULTS: Genome-wide analysis identified 241 expansin genes in the wheat genome, which were grouped into three subfamilies (EXPA, EXPB and EXLA) by phylogenetic tree. Molecular structure analysis showed that wheat expansin gene family showed high evolutionary conservation although some differences were present in different subfamilies. Some key amino acid sites that contribute to functional divergence, positive selection, and coevolution were detected. Evolutionary analysis revealed that wheat expansin gene superfamily underwent strong positive selection. The transcriptome map and qRT-PCR analysis found that wheat expansin genes had tissue/organ expression specificity and preference, and generally highly expressed in the roots. The expression levels of some expansin genes were significantly induced by NaCl and polyethylene glycol stresses, which was consistent with the differential distribution of the cis-elements in the promoter region. CONCLUSIONS: Wheat expansin gene family showed high evolutionary conservation and wide range of functional divergence. Different selection constraints may influence the evolution of the three expansin subfamilies. The different expression patterns demonstrated that expansin genes could play important roles in plant growth and abiotic stress responses. This study provides new insights into the structures, evolution and functions of wheat expansin gene family. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5455-1) contains supplementary material, which is available to authorized users. BioMed Central 2019-02-01 /pmc/articles/PMC6359794/ /pubmed/30709338 http://dx.doi.org/10.1186/s12864-019-5455-1 Text en © The Author(s). 2019 Open Access This 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
Han, Zhisheng
Liu, Yanlin
Deng, Xiong
Liu, Dongmiao
Liu, Yue
Hu, Yingkao
Yan, Yueming
Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)
title Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)
title_full Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)
title_fullStr Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)
title_full_unstemmed Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)
title_short Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)
title_sort genome-wide identification and expression analysis of expansin gene family in common wheat (triticum aestivum l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359794/
https://www.ncbi.nlm.nih.gov/pubmed/30709338
http://dx.doi.org/10.1186/s12864-019-5455-1
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