scholarly journals Genome-Wide Analysis of Auxin Receptor Family Genes in Brassica juncea var. tumida

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 165 ◽  
Author(s):  
Zhaoming Cai ◽  
De-er Zeng ◽  
Jingjing Liao ◽  
Chunhong Cheng ◽  
Zulfiqar Ali Sahito ◽  
...  
Keyword(s):  
Plant Growth ◽  
Brassica Juncea ◽  
Plasmodiophora Brassicae ◽  
Auxin Signaling ◽  
Auxin Receptor ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Gene Structures ◽  
Receptor Family

Transport inhibitor response 1/auxin signaling f-box proteins (TIR1/AFBs) play important roles in the process of plant growth and development as auxin receptors. To date, no information has been available about the characteristics of the TIR1/AFB gene family in Brassica juncea var. tumida. In this study, 18 TIR1/AFB genes were identified and could be clustered into six groups. The genes are located in 11 of 18 chromosomes in the genome of B. juncea var. tumida, and similar gene structures are found for each of those genes. Several cis-elements related to plant response to phytohormones, biotic stresses, and abiotic stresses are found in the promoter of BjuTIR1/AFB genes. The results of qPCR analysis show that most genes have differential patterns of expression among six tissues, with the expression levels of some of the genes repressed by salt stress treatment. Some of the genes are also responsive to pathogen Plasmodiophora brassicae treatment. This study provides valuable information for further studies as to the role of BjuTIR1/AFB genes in the regulation of plant growth, development, and response to abiotic stress.

scholarly journals Expression and Role of Biosynthetic, Transporter, Receptor, and Responsive Genes for Auxin Signaling during Clubroot Disease Development

2020 ◽  
Vol 21 (15) ◽  
pp. 5554
Author(s):  
Arif Hasan Khan Robin ◽  
Gopal Saha ◽  
Rawnak Laila ◽  
Jong-In Park ◽  
Hoy-Taek Kim ◽  
...  
Keyword(s):  
Plasmodiophora Brassicae ◽  
Fold Increase ◽  
Auxin Signaling ◽  
Post Inoculation ◽  
Disease Development ◽  
Secondary Phases ◽  
Auxin Receptor ◽  
Clubroot Disease ◽  
Root Tissues

Auxins play a pivotal role in clubroot development caused by the obligate biotroph Plasmodiophora brassicae. In this study, we investigated the pattern of expression of 23 genes related to auxin biosynthesis, reception, and transport in Chinese cabbage (Brassica rapa) after inoculation with P. brassicae. The predicted proteins identified, based on the 23 selected auxin-related genes, were from protein kinase, receptor kinase, auxin responsive, auxin efflux carrier, transcriptional regulator, and the auxin-repressed protein family. These proteins differed in amino acids residue, molecular weights, isoelectric points, chromosomal location, and subcellular localization. Leaf and root tissues showed dynamic and organ-specific variation in expression of auxin-related genes. The BrGH3.3 gene, involved in auxin signaling, exhibited 84.4-fold increase in expression in root tissues compared to leaf tissues as an average of all samples. This gene accounted for 4.8-, 2.6-, and 5.1-fold higher expression at 3, 14, and 28 days post inoculation (dpi) in the inoculated root tissues compared to mock-treated roots. BrNIT1, an auxin signaling gene, and BrPIN1, an auxin transporter, were remarkably induced during both cortex infection at 14 dpi and gall formation at 28 dpi. BrDCK1, an auxin receptor, was upregulated during cortex infection at 14 dpi. The BrLAX1 gene, associated with root hair development, was induced at 1 dpi in infected roots, indicating its importance in primary infection. More interestingly, a significantly higher expression of BrARP1, an auxin-repressed gene, at both the primary and secondary phases of infection indicated a dynamic response of the host plant towards its resistance against P. brassicae. The results of this study improve our current understanding of the role of auxin-related genes in clubroot disease development.

scholarly journals Genome-wide analysis and expression characteristics of small auxin-up RNA (SAUR) genes in moso bamboo (Phyllostachys edulis)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 325-336 ◽  
Author(s):  
Qingsong Bai ◽  
Dan Hou ◽  
Long Li ◽  
Zhanchao Cheng ◽  
Wei Ge ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Shoot Growth ◽  
Subcellular Location ◽  
Moso Bamboo ◽  
Pcr Analysis ◽  
Phyllostachys Edulis ◽  
Comprehensive Overview ◽  
Genome Wide ◽  
Gene Structures

Moso bamboo (Phyllostachys edulis) is well known for its rapid shoot growth. Auxin exerts pleiotropic effects on plant growth. The small auxin-up RNA (SAUR) genes are early auxin-responsive genes involved in plant growth. In total, 38 SAUR genes were identified in P. edulis (PheSAUR). A comprehensive overview of the PheSAUR gene family is presented, including the gene structures, phylogeny, and subcellular location predictions. A transcriptome analysis indicated that 37 (except PheSAUR18) of the PheSAUR genes were expressed during shoot growth process and that the PheSAUR genes were differentially expressed. Furthermore, quantitative real-time PCR analysis indicated that all of the PheSAUR genes could be induced in different tissues of seedlings and that 37 (except PheSAUR41) of the PheSAUR genes were up-regulated after indole-3-acetic acid (IAA) treatment. These results reveal a comprehensive overview of the PheSAUR gene family and may pave the way for deciphering their functions during bamboo development.

scholarly journals A synthetic approach reveals a highly sensitive maize auxin response circuit

2019 ◽  
Author(s):  
Román Ramos Báez ◽  
Yuli Buckley ◽  
Han Yu ◽  
Zongliang Chen ◽  
Andrea Gallavotti ◽  
...  
Keyword(s):  
Auxin Signaling ◽  
Synthetic Approach ◽  
Auxin Response ◽  
Auxin Receptor ◽  
Repressor Proteins ◽  
Highly Sensitive ◽  
Signaling Function ◽  
Wide Range ◽  
Signaling Components

Auxin plays a key role across all land plants in growth and developmental processes. Although auxin signaling function has diverged and expanded, differences in the molecular functions of signaling components have largely been characterized in Arabidopsis thaliana. Here, we used the Auxin Response Circuit recapitulated in Saccharomyces cerevisiae (ARCSc) system to functionally annotate maize auxin signaling components, focusing on genes expressed during development of ear and tassel inflorescences. All 16 maize Auxin (Aux)/Indole-3-Acetic Acid (IAA) repressor proteins are degraded in response to auxin, with rates that depended on both receptor and repressor identity. When fused to the maize TOPLESS (TPL) homolog RAMOSA1 ENHANCER LOCUS2 (REL2), maize Aux/IAAs were able to repress AUXIN RESPONSE FACTOR (ARF) transcriptional activity. A complete auxin response circuit comprised of all maize components, including ZmAFB2/3 b1 maize AUXIN SIGNALING F-BOX (AFB) receptor, was found to be fully functional. The ZmAFB2/3 b1 auxin receptor was found to be more sensitive to hormone than AtAFB2 and allowed for rapid circuit activation upon auxin addition. These results validate the conserved role of predicted auxin response genes in maize, as well as provide evidence that a synthetic approach can facilitate broader comparative studies across the wide range of species with sequenced genomes.

scholarly journals Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7950 ◽  
Author(s):  
Yongbin Wang ◽  
Lei Ling ◽  
Zhenfeng Jiang ◽  
Weiwei Tan ◽  
Zhaojun Liu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Genomic Data ◽  
Evolutionary Analysis ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
Genome Wide ◽  
Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

scholarly journals Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mengyuan Wei ◽  
Aili Liu ◽  
Yujuan Zhang ◽  
Yong Zhou ◽  
Donghua Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Genome Wide ◽  
Gene Structures ◽  
Relationship Of ◽  
Zip Genes

Abstract Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

scholarly journals Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis

2022 ◽  
Vol 12 ◽  
Author(s):  
Bobin Liu ◽  
Juanli Zhu ◽  
Lina Lin ◽  
Qixin Yang ◽  
Bangping Hu ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Southern China ◽  
Gene Families ◽  
Auxin Signaling ◽  
Auxin Response ◽  
Chromosomal Distribution ◽  
Element Analysis ◽  
Genome Wide ◽  
Gene Structures

Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.

scholarly journals BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Akram Ali Baloch ◽  
Agha Muhammad Raza ◽  
Shahjahan Shabbir Ahmed Rana ◽  
Saad Ullah ◽  
Samiullah Khan ◽  
...  
Keyword(s):  
Gene Family ◽  
Pseudomonas Syringae ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Evolutionary Model ◽  
Phylogenetic Groups ◽  
Genome Wide ◽  
Physico Chemical ◽  
Gene Structures

AbstractCNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.

scholarly journals Identification and Expression of SAUR Genes in the CAM Plant Agave

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 555
Author(s):  
Gang Deng ◽  
Xing Huang ◽  
Li Xie ◽  
Shibei Tan ◽  
Thomas Gbokie ◽  
...  
Keyword(s):  
Plant Growth ◽  
Stress Responses ◽  
Growth And Development ◽  
Developmental Stages ◽  
Auxin Signaling ◽  
Plant Growth And Development ◽  
Cam Plants ◽  
African Countries ◽  
Biotic Stresses ◽  
Species Specific

Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber production in Brazil, China, and African countries. Small Auxin Up-regulated RNA (SAUR) genes have broad effect on auxin signaling-regulated plant growth and development, while only few SAUR genes have been reported in Agave species. In this study, we identified 43, 60, 24, and 21 SAUR genes with full-length coding regions in A. deserti, A. tequilana, A. H11648, and A. americana, respectively. Although phylogenetic analysis revealed that rice contained a species-specific expansion pattern of SAUR gene, no similar phenomena were observed in Agave species. The in silico expression indicated that SAUR genes had a distinct expression pattern in A. H11648 compared with other Agave species; and four SAUR genes were differentially expressed during CAM diel cycle in A. americana. Additionally, an expression analysis was conducted to estimate SAUR gene expression during different leaf developmental stages, abiotic and biotic stresses in A. H11648. Together, we first characterized the SAUR genes of Agave based on previously published transcriptome datasets and emphasized the potential functions of SAUR genes in Agave’s leaf development and stress responses. The identification of which further expands our understanding on auxin signaling-regulated plant growth and development in Agave species.

scholarly journals Host auxin machinery is important in mediating root architecture changes induced by Pseudomonas fluorescens GM30 and Serendipita indica

2020 ◽  
Author(s):  
Anna Matthiadis ◽  
Poornima Sukumar ◽  
Alyssa DeLeon ◽  
Dale Pelletier ◽  
Jessy L. Labbé ◽  
...  
Keyword(s):  
Plant Growth ◽  
Lateral Root ◽  
Root Architecture ◽  
Fungal Species ◽  
Root Production ◽  
Auxin Signaling ◽  
Beneficial Microbes ◽  
Plant Growth Promoting ◽  
Growth Promoting

AbstractAuxin is a key phytohormone that is integral to plant developmental processes including those underlying root initiation, elongation, and branching. Beneficial microbes have been shown to have an impact on root development, potentially mediated through auxin. In this study, we explore the role of host auxin signaling and transport components in mediating the root growth promoting effects of beneficial microbes. Towards this end, we undertook co-culture studies of Arabidopsis thaliana plants with microbes previously reported to promote lateral root proliferation and produce auxin. Two types of beneficial microbes were included in the present study; a plant growth promoting bacterial species of interest, Pseudomonas fluorescens GM30, and a well-studied plant growth promoting fungal species, Serendipita indica (Piriformospora indica). Following co-culture, lateral root production was found restored in auxin transport inhibitor-treated plants, suggesting involvement of microbe and/or microbially-produced auxin in altering plant auxin levels. In order to clarify the role of host auxin signaling and transport pathways in mediating interactions with bacterial and fungal species, we employed a suite of auxin genetic mutants as hosts in co-culture screens. Our result show that the transport proteins PIN2, PIN3, and PIN7 and the signaling protein ARF19, are required for mediating root architecture effects by the bacterial and/or fungal species. Mutants corresponding to these proteins did not significantly respond to co-culture treatment and did not show increases in lateral root production and lateral root density. These results implicate the importance of host auxin signaling in both bacterial and fungal induced changes in root architecture and serve as a driver for future research on understanding the role of auxin-dependent and auxin-independent pathways in mediating plant-microbe interactions in economically important crop species.

scholarly journals Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process

2021 ◽  
Vol 12 ◽  
Author(s):  
Suyun Wei ◽  
Yingnan Chen ◽  
Jing Hou ◽  
Yonghua Yang ◽  
Tongming Yin
Keyword(s):  
Plant Growth ◽  
Growth Process ◽  
Transcriptome Profiling ◽  
Gene Families ◽  
Auxin Signaling ◽  
Vascular Differentiation ◽  
Auxin Signaling Pathway ◽  
Functional Involvement ◽  
Functional Features ◽  
Gene Structures

The phytohormone auxin plays a pivotal role in the regulation of plant growth and development, including vascular differentiation and tree growth. The auxin/indole-3-acetic acid (Aux/IAA) and auxin response transcription factor (ARF) genes are key components of plant auxin signaling. To gain more insight into the regulation and functional features of Aux/IAA and ARF genes during these processes, we identified 38 AUX/IAA and 34 ARF genes in the genome of Salix suchowensis and characterized their gene structures, conserved domains, and encoded amino acid compositions. Phylogenetic analysis of some typical land plants showed that the Aux/IAA and ARF genes of Salicaceae originated from a common ancestor and were significantly amplified by the ancestral eudicot hexaploidization event and the “salicoid” duplication that occurred before the divergence of poplar and willow. By analyzing dynamic transcriptome profiling data, some Aux/IAA and ARF genes were found to be involved in the regulation of plant growth, especially in the initial plant growth process. Additionally, we found that the expression of several miR160/miR167-ARFs was in agreement with canonical miRNA–ARF interactions, suggesting that miRNAs were possibly involved in the regulation of the auxin signaling pathway and the plant growth process. In summary, this study comprehensively analyzed the sequence features, origin, and expansion of Aux/IAA and ARF genes, and the results provide useful information for further studies on the functional involvement of auxin signaling genes in the plant growth process.

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