Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit

The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically...

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Autores principales:	Muhammad Aamir Manzoor, Irfan Ali Sabir, Iftikhar Hussain Shah, Han Wang, Zhao Yu, Faiz Rasool, Muhammad Zaid Mazhar, Shoaib Younas, Muhammad Abdullah, Yongping Cai
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	GATA transcription factor evolution phylogenetic analysis subcellular localization abiotic stress gene expression Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/a0c05735d93146a592f342529c833c14
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spelling	oai:doaj.org-article:a0c05735d93146a592f342529c833c142021-11-25T17:57:13ZComprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit10.3390/ijms2222124921422-00671661-6596https://doaj.org/article/a0c05735d93146a592f342529c833c142021-11-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/22/12492https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically studied in many species, less is known about GATA genes in Chinese pears (<i>Pyrus bretschneideri</i>). In the current study, the GATA gene family in the four Rosaceae genomes was identified, its structural characteristics identified, and a comparative analysis of its properties was carried out. Ninety-two encoded GATA proteins were authenticated in the four Rosaceae genomes (<i>Pyrus bretschneideri</i>, <i>Prunus avium</i>, <i>Prunus mume</i>, and <i>Prunus persica</i>) and categorized into four subfamilies (Ⅰ–Ⅳ) according to phylogeny. The majority of GATA genes contained one to two introns and conserved motif composition analysis revealed their functional divergence. Whole-genome duplications (WGDs) and dispersed duplication (DSD) played a key role in the expansion of the GATA gene family. The microarray indicated that, among <i>P. bretschneideri</i>, <i>P. avium</i>, <i>P. mume</i> and <i>P. persica</i>, GATA duplicated regions were more conserved between <i>Pyrus bretschneideri</i> and <i>Prunus persica</i> with 32 orthologous genes pairs. The physicochemical parameters, duplication patterns, non-synonymous (ka), and synonymous mutation rate (ks) and GO annotation ontology were performed using different bioinformatics tools. <i>cis</i>-elements respond to various phytohormones, abiotic/biotic stress, and light-responsive were found in the promoter regions of GATA genes which were induced via stimuli. Furthermore, subcellular localization of the <i>PbGATA22</i> gene product was investigated, showing that it was present in the nucleus of tobacco (<i>Nicotiana tabacum</i>) epidermal cells. Finally, in silico analysis was performed on various organs (bud, leaf, stem, ovary, petal, and sepal) and different developmental stages of fruit. Subsequently, the expression profiles of <i>PbGATA</i> genes were extensively expressed under exogenous hormonal treatments of SA (salicylic acid), MeJA (methyl jasmonate), and ABA (abscisic acid) indicating that play important role in hormone signaling pathways. A comprehensive analysis of GATA transcription factors was performed through systematic biological approaches and comparative genomics to establish a theoretical base for further structural and functional investigations in Rosaceae species.Muhammad Aamir ManzoorIrfan Ali SabirIftikhar Hussain ShahHan WangZhao YuFaiz RasoolMuhammad Zaid MazharShoaib YounasMuhammad AbdullahYongping CaiMDPI AGarticleGATA transcription factorevolutionphylogenetic analysissubcellular localizationabiotic stressgene expressionBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 12492, p 12492 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	GATA transcription factor evolution phylogenetic analysis subcellular localization abiotic stress gene expression Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	GATA transcription factor evolution phylogenetic analysis subcellular localization abiotic stress gene expression Biology (General) QH301-705.5 Chemistry QD1-999 Muhammad Aamir Manzoor Irfan Ali Sabir Iftikhar Hussain Shah Han Wang Zhao Yu Faiz Rasool Muhammad Zaid Mazhar Shoaib Younas Muhammad Abdullah Yongping Cai Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit
description	The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically studied in many species, less is known about GATA genes in Chinese pears (<i>Pyrus bretschneideri</i>). In the current study, the GATA gene family in the four Rosaceae genomes was identified, its structural characteristics identified, and a comparative analysis of its properties was carried out. Ninety-two encoded GATA proteins were authenticated in the four Rosaceae genomes (<i>Pyrus bretschneideri</i>, <i>Prunus avium</i>, <i>Prunus mume</i>, and <i>Prunus persica</i>) and categorized into four subfamilies (Ⅰ–Ⅳ) according to phylogeny. The majority of GATA genes contained one to two introns and conserved motif composition analysis revealed their functional divergence. Whole-genome duplications (WGDs) and dispersed duplication (DSD) played a key role in the expansion of the GATA gene family. The microarray indicated that, among <i>P. bretschneideri</i>, <i>P. avium</i>, <i>P. mume</i> and <i>P. persica</i>, GATA duplicated regions were more conserved between <i>Pyrus bretschneideri</i> and <i>Prunus persica</i> with 32 orthologous genes pairs. The physicochemical parameters, duplication patterns, non-synonymous (ka), and synonymous mutation rate (ks) and GO annotation ontology were performed using different bioinformatics tools. <i>cis</i>-elements respond to various phytohormones, abiotic/biotic stress, and light-responsive were found in the promoter regions of GATA genes which were induced via stimuli. Furthermore, subcellular localization of the <i>PbGATA22</i> gene product was investigated, showing that it was present in the nucleus of tobacco (<i>Nicotiana tabacum</i>) epidermal cells. Finally, in silico analysis was performed on various organs (bud, leaf, stem, ovary, petal, and sepal) and different developmental stages of fruit. Subsequently, the expression profiles of <i>PbGATA</i> genes were extensively expressed under exogenous hormonal treatments of SA (salicylic acid), MeJA (methyl jasmonate), and ABA (abscisic acid) indicating that play important role in hormone signaling pathways. A comprehensive analysis of GATA transcription factors was performed through systematic biological approaches and comparative genomics to establish a theoretical base for further structural and functional investigations in Rosaceae species.
format	article
author	Muhammad Aamir Manzoor Irfan Ali Sabir Iftikhar Hussain Shah Han Wang Zhao Yu Faiz Rasool Muhammad Zaid Mazhar Shoaib Younas Muhammad Abdullah Yongping Cai
author_facet	Muhammad Aamir Manzoor Irfan Ali Sabir Iftikhar Hussain Shah Han Wang Zhao Yu Faiz Rasool Muhammad Zaid Mazhar Shoaib Younas Muhammad Abdullah Yongping Cai
author_sort	Muhammad Aamir Manzoor
title	Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit
title_short	Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit
title_full	Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit
title_fullStr	Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit
title_full_unstemmed	Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit
title_sort	comprehensive comparative analysis of the gata transcription factors in four rosaceae species and phytohormonal response in chinese pear (<i>pyrus bretschneideri</i>) fruit
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/a0c05735d93146a592f342529c833c14
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Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (<i>Pyrus bretschneideri</i>) Fruit

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