Genome-wide identification of auxin response factors (ARFs) in three different species of Arachis

2021 ◽  
Author(s):  
Bikash Raul ◽  
Oindrila Bhattacharjee ◽  
Kunal Tembhare ◽  
Tanyya Khanna ◽  
Tarannum Shaheen ◽  
...  
Keyword(s):  
Auxin Response ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Genome Wide

scholarly journals Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 24
Author(s):  
Jianfei Wu ◽  
Fan Gao ◽  
Tongtong Li ◽  
Haixia Guo ◽  
Li Zhang ◽  
...  
Keyword(s):  
Target Genes ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Auxin Response ◽  
Higher Plant ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Genome Wide ◽  
A Genome ◽  
Almost All

Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information.

scholarly journals Genome-wide identification and expression analysis of auxin response factors in peanut (Arachis hypogaea L.)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12319
Author(s):  
Peipei Li ◽  
Qian Ma ◽  
Chengxin Qu ◽  
Shuliang Zhu ◽  
Kunkun Zhao ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Plant Growth And Development ◽  
Auxin Response ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Genome Data ◽  
Genome Wide ◽  
Arachis Hypogaea L ◽  
Pod Development ◽  
Cultivated Species

Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I–VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.

Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa)

Gene ◽  
2007 ◽  
Vol 394 (1-2) ◽  
pp. 13-24 ◽  
Author(s):  
Dekai Wang ◽  
Kemei Pei ◽  
Yaping Fu ◽  
Zongxiu Sun ◽  
Sujuan Li ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Auxin Response ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Parallel structural evolution of auxin response factors in the angiosperms

2010 ◽  
Vol 63 (6) ◽  
pp. 952-959 ◽  
Author(s):  
Cédric Finet ◽  
Chloé Fourquin ◽  
Marion Vinauger ◽  
Annick Berne-Dedieu ◽  
Pierre Chambrier ◽  
...  
Keyword(s):  
Structural Evolution ◽  
Auxin Response ◽  
Response Factors ◽  
Auxin Response Factors

scholarly journals Noncoding RNAs, Emerging Regulators in Root Endosymbioses

2016 ◽  
Vol 29 (3) ◽  
pp. 170-180 ◽  
Author(s):  
Christine Lelandais-Brière ◽  
Jérémy Moreau ◽  
Caroline Hartmann ◽  
Martin Crespi
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Plant Root ◽  
Arbuscular Mycorrhizal ◽  
Auxin Response ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Control Gene Expression ◽  
Small Ncrnas ◽  
Am Symbiosis

Endosymbiosis interactions allow plants to grow in nutrient-deficient soil environments. The arbuscular mycorrhizal (AM) symbiosis is an ancestral interaction between land plants and fungi, whereas nitrogen-fixing symbioses are highly specific for certain plants, notably major crop legumes. The signaling pathways triggered by specific lipochitooligosaccharide molecules involved in these interactions have common components that also overlap with plant root development. These pathways include receptor-like kinases, transcription factors (TFs), and various intermediate signaling effectors, including noncoding (nc)RNAs. These latter molecules have emerged as major regulators of gene expression and small ncRNAs, composed of micro (mi)RNAs and small interfering (si)RNAs, are known to control gene expression at transcriptional (chromatin) or posttranscriptional levels. In this review, we describe exciting recent data connecting variants of conserved si/miRNAs with the regulation of TFs, such as NSP2, NFY-A1, auxin-response factors, and AP2-like proteins, known to be involved in symbiosis. The link between hormonal regulations and these si- and miRNA-TF nodes is proposed in a model in which different feedback loops or regulations controlling endosymbiosis signaling are integrated. The diversity and emerging regulatory networks of young legume miRNAs are also highlighted.

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