Petunia
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA305984 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Petunia floral scent production and emission is highly regulated, with a major role for the transcription factor ODORANT1 (ODO1) in directing activation of volatile biosynthesis. Using ChIP-seq of tagged ODO1 protein from petunia flowers, and RNA-seq of wild-type and odo1i RNAi flowers, the ODORANT1-regulated gene network of petunia is described, which extends to branches involved in phenylpropanoid intermediate production and S-adenosyl-methionine biosynthesis to potentiate production and emission of volatiles. Analysis of direct targets of regulation has also enabled the identification of an ODO1 binding motif.
2021-11-22 | GSE189280 | GEO
Project description:Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome-wide expression analysis has been rarely applied because of the lack of sequence information. We applied next-generation sequencing to generate, through de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. On the basis of the transcriptome of each species, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global- and organ-specific gene expression in both species. In addition, microarray analysis was applied to explore the molecular basis of the seed coat defects in Petunia hybrida mutants, homozygous for a null allele of the AN11 gene, encoding a WDR transcription regulator. Among the transcripts differentially expressed in an11 seeds compared to wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next-generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in P. axillaris, P. inflata and P. hybrida.
2012-02-29 | GSE28120 | GEO
Project description:Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome-wide expression analysis has been rarely applied because of the lack of sequence information. We applied next-generation sequencing to generate, through de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. On the basis of the transcriptome of each species, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global- and organ-specific gene expression in both species. In addition, microarray analysis was applied to explore the molecular basis of the seed coat defects in Petunia hybrida mutants, homozygous for a null allele of the AN11 gene, encoding a WDR transcription regulator. Among the transcripts differentially expressed in an11 seeds compared to wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next-generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in P. axillaris, P. inflata and P. hybrida. The manuscript describes the creation by next generation sequencing of a large catalogue of the transcriptome of the two Petunia species, that are considered to represent the natural material from which the breeders selected their varieties. This submission represents the transcriptome component of study. The high throughput sequencing data were submitted to SRA (accession numbers: SRA027293, SRP004866.1, SRX036999.2, SRX036998.2).
2012-02-29 | E-GEOD-28120 | biostudies-arrayexpress
Project description:White areas of star-type bicolor petals of petunia (Petunia hybrida) are caused by post-transcriptional gene silencing (PTGS) of the key enzyme of anthocyanin biosynthesis. We observed blotched flowers and vein-clearing symptom in leaves in 3- to 4-month-old petunia plants. In order to determine the cause of blotched flowers, we examined an endogenous pararetrovirus, petunia vein clearing virus (PVCV), because this virus causes vein-clearing symptom and may have a suppressor of PTGS. Transcripts and episomal DNA derived from proviral PVCV loci highly accumulated in 3- to 4-month-old plants, indicating that PVCV was activated as the host plant ages. Furthermore, CG and CHG sites of the promoter region of PVCV were highly methylated in 1-month-old plants but these cytosines were not methylated in 3- to 4-month-old plants, suggesting that poor maintenance of DNA methylation activates propagation of PVCV. In parallel, de novo methylation at CHH sites and 24-nt small RNAs were detected on the promoter region of PVCV, indicating that RNA-directed DNA methylation was induced by PVCV activation. Detections of transcripts and episomal DNA of PVCV in blotched regions and suppressor activity of PTGS support the mechanism that suppression of PTGS by activated PVCV causes blotched flowers.
2020-02-18 | GSE145373 | GEO
Project description:Petunia axillaris x Petunia exserta RILs Raw sequence reads
| PRJNA704924 | ENA
Project description:To better understand how diurnal transcriptional regulation contributes to day/night cycles of volatile emission from the petunia flower, cross-linked chromatin from corolla in the morning (7AM) and evening (7PM) was immunoprecipitated with antibodies against 4 histone marks associated with trancriptional activity to determine islands enriched for the marks in morning and evening.
2023-11-08 | GSE230857 | GEO
Project description:N1-methyladenosine is a unique base methylation because it blocks Watson-Crick base paring and introduces a positive charge. Previous studies showed that m1A is prevalent in yeast and mammals mRNA and has a functional role in promoting translation of methylated mRNA. However, little is known about its abundance, topology and dynamics in plant mRNA. In this study, dot blotting and LC–MS/MS analyses reveal a dynamic pattern of m1A mRNA modification in various tissues and at different developmental stages in petunia (Petunia hybrida). Transcriptome-wide profiling of mRNA m1A in petunia was reported by applying m1A mRNA immunoprecipitation followed by a deep-sequencing approach (m1A-seq). m1A-seq analysis identified 4993 m1A peaks in 3231 expressed genes in petunia corollas. Each methylated gene averagely carries 1.55 peaks. Among the identified m1A peaks, there are 251 m1A peaks in which the adenines was partly replaced by thymine (T) and/or the reverse transcription stops happened in adenine site, in 199 expressed genes. We found that m1A is enriched in coding sequences with one peaks located immediately after start codons, and a slight negative correlation between methylated genes and gene expression was observed. Totally, ethylene treatment reduced the m1A level of mRNA in petunia corollas. We show that a RNA m1A-methyltransferase, tRNA specific methyltransferase 61A (PhTRMT61A), is an m1A mRNA methyltransferase. PhTRMT61A silencing results in decreased m1A peaks in mRNA in leaves and abnormal leaf development. PhTRMT61A is located to the nucleus. Our results suggest that m1A in mRNA is an important epitranscriptome marker and plays a role in plant development.
2020-08-12 | GSE136921 | GEO