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Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut

Auxin response factors (ARF) are important transcription factors which mediate the transcription of auxin responsive genes by binding directly to auxin response elements (AuxREs) found in the promoter regions of these genes. To date, no information has been available about the genome-wide organizati...

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Autores principales: Tang, Yuehui, Bao, Xinxin, Liu, Kun, Wang, Jian, Zhang, Ju, Feng, Youwei, Wang, Yangyang, Lin, Luoxiao, Feng, Jingcheng, Li, Chengwei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6070241/
https://www.ncbi.nlm.nih.gov/pubmed/30067784
http://dx.doi.org/10.1371/journal.pone.0201024
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author Tang, Yuehui
Bao, Xinxin
Liu, Kun
Wang, Jian
Zhang, Ju
Feng, Youwei
Wang, Yangyang
Lin, Luoxiao
Feng, Jingcheng
Li, Chengwei
author_facet Tang, Yuehui
Bao, Xinxin
Liu, Kun
Wang, Jian
Zhang, Ju
Feng, Youwei
Wang, Yangyang
Lin, Luoxiao
Feng, Jingcheng
Li, Chengwei
author_sort Tang, Yuehui
collection PubMed
description Auxin response factors (ARF) are important transcription factors which mediate the transcription of auxin responsive genes by binding directly to auxin response elements (AuxREs) found in the promoter regions of these genes. To date, no information has been available about the genome-wide organization of the ARF transcription factor family in physic nut. In this study, 17 ARF genes (JcARFs) are identified in the physic nut genome. A detailed investigation into the physic nut ARF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under various conditions. Phylogenetic analysis suggests that the 17 JcARF proteins are clustered into 6 groups, and most JcARF proteins from the physic nut reveal closer relationships with those from Arabidopsis than those from rice. Of the 17 JcARF genes, eight are predicted to be the potential targets of small RNAs; most of the genes show differential patterns of expression among four tissues (root, stem cortex, leaf, and seed); and qRT-PCR indicates that the expression of all JcARF genes is inhibited or induced in response to exogenous auxin. Expression profile analysis based on RNA-seq data shows that in leaves, 11 of the JcARF genes respond to at least one abiotic stressor (drought and/or salinity) at, as a minimum, at least one time point. Our results provide valuable information for further studies on the roles of JcARF genes in regulating physic nut's growth, development and responses to abiotic stress.
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spelling pubmed-60702412018-08-09 Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut Tang, Yuehui Bao, Xinxin Liu, Kun Wang, Jian Zhang, Ju Feng, Youwei Wang, Yangyang Lin, Luoxiao Feng, Jingcheng Li, Chengwei PLoS One Research Article Auxin response factors (ARF) are important transcription factors which mediate the transcription of auxin responsive genes by binding directly to auxin response elements (AuxREs) found in the promoter regions of these genes. To date, no information has been available about the genome-wide organization of the ARF transcription factor family in physic nut. In this study, 17 ARF genes (JcARFs) are identified in the physic nut genome. A detailed investigation into the physic nut ARF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under various conditions. Phylogenetic analysis suggests that the 17 JcARF proteins are clustered into 6 groups, and most JcARF proteins from the physic nut reveal closer relationships with those from Arabidopsis than those from rice. Of the 17 JcARF genes, eight are predicted to be the potential targets of small RNAs; most of the genes show differential patterns of expression among four tissues (root, stem cortex, leaf, and seed); and qRT-PCR indicates that the expression of all JcARF genes is inhibited or induced in response to exogenous auxin. Expression profile analysis based on RNA-seq data shows that in leaves, 11 of the JcARF genes respond to at least one abiotic stressor (drought and/or salinity) at, as a minimum, at least one time point. Our results provide valuable information for further studies on the roles of JcARF genes in regulating physic nut's growth, development and responses to abiotic stress. Public Library of Science 2018-08-01 /pmc/articles/PMC6070241/ /pubmed/30067784 http://dx.doi.org/10.1371/journal.pone.0201024 Text en © 2018 Tang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Tang, Yuehui
Bao, Xinxin
Liu, Kun
Wang, Jian
Zhang, Ju
Feng, Youwei
Wang, Yangyang
Lin, Luoxiao
Feng, Jingcheng
Li, Chengwei
Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut
title Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut
title_full Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut
title_fullStr Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut
title_full_unstemmed Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut
title_short Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut
title_sort genome-wide identification and expression profiling of the auxin response factor (arf) gene family in physic nut
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6070241/
https://www.ncbi.nlm.nih.gov/pubmed/30067784
http://dx.doi.org/10.1371/journal.pone.0201024
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