Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of ARF and Aux/IAA expression during the induction of somatic embryogenesis in Coffea canephora

ABSTRACT: Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. The results of this study allow to have a better understanding of the genes involved in auxin signaling pathway as well as their expression profiles during the SE process.

ORGANISM(S): Coffea canephora

PROVIDER: GSE128888 | GEO | 2019/04/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

Project description:We used a next-generation sequencing approach, Illumina Digital Gene Expression (DGE) technology, to Genome-wide profiling of gene expression during cotton SE. As a result, 5,076 differentially expressed genes were identified during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process. Transcription factor-encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein / indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE. We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis. differential gene expression analysis at 9 time-points/stages during somatic embryogenesis in cotton by deep sequencing, using Illumina GAIIx.

2012-05-31 | E-GEOD-38209 | biostudies-arrayexpress

Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

2012-05-31 | GSE38209 | GEO

Transcriptional profiles between mp mutant seedlings and transgenics carrying the dexamethasone-inducible GR-bdl protein

2010-04-01 | GSE13881 | GEO

Variation in auxin sensing guides AUX/IAA repressor ubiquitylation and destruction

Project description:Auxin is a drug-like small molecule and morphogen that triggers the formation of SCFTIR1/AFB-AUX/IAA co-receptor complexes leading to ubiquitylation and proteasome-dependent degradation of AUX/IAA transcriptional repressors in plants. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. TIR1-IAA19 and TIR1-IAA6 interactions form co-receptors with different affinities, which specify ubiquitylation and turnover rate of the AUX/IAA. We demonstrate lysine ubiquitylation in IAA6/IAA19 and propose this ubiquitylation signature to be a consequence of auxin-mediated SCFTIR1-AUX/IAA interactions. We present evidence for an evolving AUX/IAA repertoire, typified by the IAA6/IAA19 ohnologs, that contributes differentially to auxin sensing. We postulate that AUX/IAAs have emerged as a versatility toolbox for auxin-modulated transcriptional control, as the gamut of AUX/IAA destruction kinetics enables fine-tuning of transcriptional auxin response and contributes to the complexity of hormone signaling.

2017-06-14 | PXD004027 | Pride

Analysis of the effect of exogenous auxin on the regulatory relationship between miRNA and its target genes in rose using high-throughput sequencing

Project description:Rose (Rosa hybrida L.) is a major cut flowers in the world. Studying the molecular mechanism of auxin regulation in growth is of great significance for enhancing the understanding of the growth and development processes of rose and informing accurate exogenous auxin application in rose production. However, the response mechanism of rose to miRNA-mediated auxin signal transduction is unclear. In this study, rose plants were treated with IAA, and 75 known miRNAs and 168 novel miRNAs were identified by small RNA sequencing. Among them, 19 known miRNAs and 42 miRNAs were differentially expressed. Many differential miRNAs demonstrated staged responses to auxin treatment. The targeted relationship between miRNA and key transcription factors regulated by auxin in rose was analyzed, and the target genes in the ARF family and AUX/IAA family were screened. By using quantitative real-time PCR(qRT-PCR) to verify the expression patterns of the miRNA regulating the auxin signal transduction pathway and its target gene, we found that miR156a, miR160a, miR164a, miR167d, miR396b-3p, novel_miR_189, novel_miR_74, novel_miR_8, and novel_miR_207 interacted negatively with the ARF family, and miR390a-3p and novel_miR_101 interacted negatively with the AUX/IAA family. These results provide a theoretical basis for further studies on the auxin regulatory mechanisms in rose.

2023-02-28 | GSE225844 | GEO

Analysis of the effect of exogenous auxin on the regulatory relationship between miRNA and its target genes in rose using high-throughput sequencing [RNA-seq]

2024-02-24 | GSE225991 | GEO

Grigolon2018 - Responses to auxin signals

Project description:Plants depend on the signalling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signalling network involves a negative feedback on Aux/IAA proteins which mediate the influence of auxin (the signal) on the auxin response factor (ARF) transcription factors (the drivers of the response). To probe the role of this feedback, we consider alternative in silico signalling networks implementing different operating principles. By a comparative analysis, we find that the presence of a negative feedback allows the system to have a far larger sensitivity in its dynamical response to auxin and that this sensitivity does not prevent the system from being highly resilient. Given this insight, we build a new biomolecular signalling model for quantitatively describing such Aux/IAA and ARF responses.

2022-05-10 | MODEL2003060002 | BioModels

Grigolon2018-Responses to auxin signals

2024-09-02 | BIOMD0000000927 | BioModels

Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

Project description:Background: Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known. Results: In this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes. Evolutionary and comparative analysis revealed that 111 (94.1%) B. napus Aux/IAA genes were multiplied due to ancestral Brassica genome triplication and recent allotetraploidy from B. rapa and B. oleracea. Phylogenetic analysis indicated seven subgroups containing 29 orthologous gene sets and two Brassica-specific gene sets. Structures of genes and proteins varied across different genes but were conserved among homologous genes in B. napus. Furthermore, analysis of transcriptional profiles revealed that the expression patterns of Aux/IAA genes in B. napus were tissue dependent. Auxin-responsive elements tend to be distributed in the proximal region of promoters, and are significantly associated with early exogenous auxin up-regulation. Conclusions: The Aux/IAA gene family were identified and analyzed comprehensively in the allotetraploid B. napus genome. This analysis provides a deeper understanding of diversification of Aux/IAA gene family and will facilitate further dissection of Aux/IAA gene function in B. napus.

2017-10-23 | GSE105889 | GEO

Transcriptional profiles between mp mutant seedlings and transgenics carrying the dexamethasone-inducible GR-bdl protein

Project description:In order to identify targets of the transcription factor AUXIN RESPONSE FACTOR5 / MONOPTEROS (ARF5/MP), we compared transcriptomes of mp-B4149 mutant seedlings (9 day-old) and seedlings carrying the dexamethasone-inducible version of the MP inhibitor protein BODENLOS (GR-bdl). Without dexamethasone (DEX) treatment, this line is identical to the wild-type, while DEX treatment leads to strong inhibition of ARF-dependent transcription. To remove all endogenous MP-inhibiting Aux/IAA proteins, we treated mp or GR-bdl seedlings during 1 hour with auxin (50 micromolar Indole-3-Acetic Acid), either with or without a pretreatment with 10 micromolar DEX for 1 hour. Genes that are activated by MP are expected to br downregulated in mp seedlings and in the GR-bdl line afer DEX treatment. We used biological duplicates for each of the three treatments. Keywords: Transcriptional profiling of transcription factor targets Mp mutant and GR-bdl seeds were germinated on solid 1/2MS media, and transferred to liquid medium after 9 days of horizontal growth. Duplicate cultures were generated for mp mutants, and quadruplicates for the GR-bdl line. 10 micromolar DEX was added to both mp cultures and to two of the GR-bdl cultures, and seedlings were gently shaken during 1 hour. Then, 50 micromolar IAA was added to all 6 cultures and seedlings were incubated with gentle shaking for another hour. Total RNA was isolated from the seedlings using a QIAgen RNeasy kit, and reverse transcription, in-vitro transcription, cRNA labling and fragemntation was done according to established methods (Schmid et al., Nature Genetics [2005] 37, 501-506). Labeled cRNA was hybridized to Arabidopsis ATH1 arrays.

2010-04-12 | E-GEOD-13881 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data