Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [RNA-seq]

ABSTRACT: Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [RNA-seq]

PROVIDER: PRJNA911293 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22691000_1.fastq.gz	Fastqsanger.gz
	SRR22691000_2.fastq.gz	Fastqsanger.gz
	SRR22691001_1.fastq.gz	Fastqsanger.gz
	SRR22691001_2.fastq.gz	Fastqsanger.gz
	SRR22691002_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

The NAC transcription factor FaRIF controls fruit ripening in strawberry

Project description:In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.

2021-02-20 | GSE167107 | GEO

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [DAP-seq]

Project description:To better understand FvRIF-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to unravel FvRIF binding sites at the genome level. For DAP-seq analysis, the recombinant FvRIF fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA ‘input’ negative control libraries were prepared and submitted for deep sequencing.

2023-11-08 | GSE220785 | GEO

The NAC transcription factor FaRIF controls fruit ripening in strawberry

Project description:The NAC transcription factor FaRIF controls fruit ripening in strawberry

| PRJNA703007 | ENA

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening

Project description:Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening

| PRJNA911320 | ENA

RdDM is involved in epigenetic regulation of strawberry fruit ripening

Project description:DNA methylation is a conserved epigenetic mark that influences diverse biological processes in many eukaryotes. Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during ripening of non-climacteric fruits, or other climacteric fruits, are unknown. Here, we generated and characterized single-base resolution maps of the DNA methylome in strawberry fruit, from immature to ripe stages. We observed an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. However, we discovered that the mechanisms underlying DNA hypomethylation during ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes were not up-regulated during ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation were down-regulated during strawberry ripening. Further, ripening-induced DNA hypomethylation was associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that DNA hypomethylation during strawberry ripening is caused by diminished RdDM activity. Finally, hundreds of ripening-related genes displayed altered expression that was associated with, and thus potentially regulated by, DNA hypomethylation during ripening. Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climateric fruit and reveal a novel function of RdDM in regulating an important process in plant development.

2018-11-13 | GSE113084 | GEO

Genome-wide study the fruit ripening associated lncRNAs in strawberry

Project description:With the development of high throughput sequencing technologies, plenty of non-coding RNAs (ncRNAs) have been discovered to play important roles in diverse plant biological processes. Although these ncRNAs extensively exist in plant, their biological functions are still remained to characterize. To obtain a comprehensive understanding of long non-coding RNA (lncRNA) function in strawberry fruit ripening progress, we performed transcriptomic analyses on the diploid strawberry Fragaria vesca in a time-course during fruit ripening. Here, we have identified 25,613 lncRNAs based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries. Among them, most of lncRNAs exhibit stage-specific expression pattern. Functional analysis on F.vesca endogenous FRUIT RIPENING-RELATED LONG ANTISENSE INTERGENIC RNA (FRILAIR) in octaploid strawberry Falandi, we found that overexpression FRILAIR can compete miR397 to regulate its target laccase genes (LACs), and it may contribute to strawberry ripening. Our findings demonstrate that FRILAIR can act as a competing endogenous RNA (ceRNA) by disturbing miR397 to repress expression level of LACs, and would be valuable for strawberry ripening.

2020-01-21 | GSE129032 | GEO

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [DAP-seq]

Project description:Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [DAP-seq]

| PRJNA911319 | ENA

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [RNA-seq]

Project description:To identify genes that are transcriptionally regulated by FvRIF during fruit ripening, we performed comparative transcriptome analysis through RNA sequencing (RNA-seq) using fruits of the wild type and the mutant lines (FvRIF-cr-6 and FvRIF-cr-13) at 28 DPA. Three independent biological replicates were applied for the RNA-seq analysis.

2023-11-08 | GSE220768 | GEO

Transcriptomic studies in the development and ripening of strawberry fruits

Project description:Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. By using a custom-made and high quality oligo microarray platform done with over 32000 probes including all of the genes actually described in the strawberry genome, we have analyzed the expression of genes during the development and ripening in the receptacles of these fruits.

2018-05-09 | GSE95300 | GEO

Role of Fragaria FaPRE1 in fruit ripening [FaPRE1-RNAi]

Project description:The role played by transcription factors in the regulation of strawberry fruit ripening process is scant. We have identified and functionally characterized FaPRE1, a non-DNA-binding bHLH transcription factor. FaPRE1 is a ripening-related transcription factor that regulates genes involved in cell architecture in strawberry fruit receptacles.

2019-10-18 | GSE125995 | GEO

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