Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia

Background Walnut is an important economic tree species with prominent economic value and ecological functions. However, in recent years, walnuts have become susceptible to drought stress, resulting in a decline in comprehensive benefits. Therefore, it is necessary to identify the regulatory molecul...

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Autores principales:	Tianyu Wang, Xiangqian Gao, Sisi Chen, Dapei Li, Shuwen Chen, Muhong Xie, Zhenggang Xu, Guiyan Yang
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	Juglans regia Ethylene response factor Bioinformatics Expression analysis Medicine R
Acceso en línea:	https://doaj.org/article/1f60eab9c2db4a17b3456ae86f95e6e2
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spelling	oai:doaj.org-article:1f60eab9c2db4a17b3456ae86f95e6e22021-11-21T15:05:15ZGenome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia10.7717/peerj.124292167-8359https://doaj.org/article/1f60eab9c2db4a17b3456ae86f95e6e22021-11-01T00:00:00Zhttps://peerj.com/articles/12429.pdfhttps://peerj.com/articles/12429/https://doaj.org/toc/2167-8359Background Walnut is an important economic tree species with prominent economic value and ecological functions. However, in recent years, walnuts have become susceptible to drought stress, resulting in a decline in comprehensive benefits. Therefore, it is necessary to identify the regulatory molecular mechanism associated with walnut response to drought. In many plants, ethylene responsive factor (ERF) gene family plays important roles in response to biotic and abiotic stress, especial drought. Therefore, the identification and characterisation of walnut ERF genes will benefit walnut with regard to the clarification of drought response mechanism as well as the management, production, and quality of plantations. Methods ‘ERF’ was compared against the walnut transcriptome, and the JrERFs with a complete open reading frame (ORF) were identified by ORF Finder. The molecular weights, amino acid residues, and theoretical isoelectric point (pI) were predicted by ExPASy. The distribution of JrERFs in chromosome locations was determined based on walnut genome data from NCBI. The intron-exon structures and conserved domains were analysed using Gene Structure Display Server 2.0 and CD-Search, accordingly. Multi-sequence alignment and a phylogenetic tree were constructed by ClustalX2.1 and MEGA7, respectively. The conserved motifs were acquired using MEME. Total RNA was isolated using the cetyltrimethylammonium ammonium bromide (CTAB) method (Yang et al., 2018). Gene expression was determined by using real-time quantitative polymerase chain reaction (qRT-PCR) analysis and calculated according to the 2−ΔΔCT method (Livak & Schmittgen, 2001). Results A total of 44 JrERFs were identified from the walnut transcriptome, whose ORFs were 450–1,239 bp in length. The molecular weights of the JrERF proteins (consisting 149–412 amino acids) were 16.81–43.71 kDa, with pI ranging from 4.8 (JrERF11) to 9.89 (JrERF03). The JrERFs can be divided into six groups (B1–B6), and among the groups, B6 contained the most number of members. Each JrERF contained 1–6 motifs and each motif comprised 9–50 amino acids. Among the motifs, motif1, motif2, and motif3 were the most abundant. More than 40% of JrERFs were up-regulated continuously when subjected to ethephon (ETH), PEG6000, and PEG6000+ETH treatments. Of all the JrERFs, JrERF11 showed the highest expression. Therefore, we conclude that walnut ERF genes are highly conserved and involved in the regulation of drought response in the presence of ETH. JrERFs are possibly important candidate genes for molecular breeding; hence, the findings of this study provides the theoretical basis for further investigation of ERF genes in walnut and other species.Tianyu WangXiangqian GaoSisi ChenDapei LiShuwen ChenMuhong XieZhenggang XuGuiyan YangPeerJ Inc.articleJuglans regiaEthylene response factorBioinformaticsExpression analysisMedicineRENPeerJ, Vol 9, p e12429 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Juglans regia Ethylene response factor Bioinformatics Expression analysis Medicine R
spellingShingle	Juglans regia Ethylene response factor Bioinformatics Expression analysis Medicine R Tianyu Wang Xiangqian Gao Sisi Chen Dapei Li Shuwen Chen Muhong Xie Zhenggang Xu Guiyan Yang Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia
description	Background Walnut is an important economic tree species with prominent economic value and ecological functions. However, in recent years, walnuts have become susceptible to drought stress, resulting in a decline in comprehensive benefits. Therefore, it is necessary to identify the regulatory molecular mechanism associated with walnut response to drought. In many plants, ethylene responsive factor (ERF) gene family plays important roles in response to biotic and abiotic stress, especial drought. Therefore, the identification and characterisation of walnut ERF genes will benefit walnut with regard to the clarification of drought response mechanism as well as the management, production, and quality of plantations. Methods ‘ERF’ was compared against the walnut transcriptome, and the JrERFs with a complete open reading frame (ORF) were identified by ORF Finder. The molecular weights, amino acid residues, and theoretical isoelectric point (pI) were predicted by ExPASy. The distribution of JrERFs in chromosome locations was determined based on walnut genome data from NCBI. The intron-exon structures and conserved domains were analysed using Gene Structure Display Server 2.0 and CD-Search, accordingly. Multi-sequence alignment and a phylogenetic tree were constructed by ClustalX2.1 and MEGA7, respectively. The conserved motifs were acquired using MEME. Total RNA was isolated using the cetyltrimethylammonium ammonium bromide (CTAB) method (Yang et al., 2018). Gene expression was determined by using real-time quantitative polymerase chain reaction (qRT-PCR) analysis and calculated according to the 2−ΔΔCT method (Livak & Schmittgen, 2001). Results A total of 44 JrERFs were identified from the walnut transcriptome, whose ORFs were 450–1,239 bp in length. The molecular weights of the JrERF proteins (consisting 149–412 amino acids) were 16.81–43.71 kDa, with pI ranging from 4.8 (JrERF11) to 9.89 (JrERF03). The JrERFs can be divided into six groups (B1–B6), and among the groups, B6 contained the most number of members. Each JrERF contained 1–6 motifs and each motif comprised 9–50 amino acids. Among the motifs, motif1, motif2, and motif3 were the most abundant. More than 40% of JrERFs were up-regulated continuously when subjected to ethephon (ETH), PEG6000, and PEG6000+ETH treatments. Of all the JrERFs, JrERF11 showed the highest expression. Therefore, we conclude that walnut ERF genes are highly conserved and involved in the regulation of drought response in the presence of ETH. JrERFs are possibly important candidate genes for molecular breeding; hence, the findings of this study provides the theoretical basis for further investigation of ERF genes in walnut and other species.
format	article
author	Tianyu Wang Xiangqian Gao Sisi Chen Dapei Li Shuwen Chen Muhong Xie Zhenggang Xu Guiyan Yang
author_facet	Tianyu Wang Xiangqian Gao Sisi Chen Dapei Li Shuwen Chen Muhong Xie Zhenggang Xu Guiyan Yang
author_sort	Tianyu Wang
title	Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia
title_short	Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia
title_full	Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia
title_fullStr	Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia
title_full_unstemmed	Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia
title_sort	genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in juglans regia
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/1f60eab9c2db4a17b3456ae86f95e6e2
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Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia

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