Petunia ODO1 ChIP-seq and RNA-seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Petunia x hybrida
PROVIDER: GSE189280 | GEO | 2021/11/22
REPOSITORIES: GEO
Similar Datasets
Project description:To better understand how diurnal transcriptional regulation contributes to day/night cycles of volatile emission from the petunia flower, RNA extracted from corolla in the morning (7AM) and evening (7PM) was sequenced to determine genes differentially expressed at the two time points.
2023-10-24 | GSE230802 | GEO
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: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:RNA-seq of Petunia open flowers for differences in scent-related genes between P. axillaris and P. exserta
| PRJNA344560 | ENA
Project description:RNA-seq of Petunia open flowers for differences in scent-related genes between P. axillaris, P. exserta & P. inflata
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Project description:Chinese narcissus is well-known monocot plants with beautiful color, fresh and sweet floral scent. A lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms of narcissus floral scent volatiles biosynthesis. Hence, we hypothesized the functions of the significant differentially expressed genes (DEGs) identified using Illumina RNA-Seq technology, according to public protein annotation databases in this study.
2020-02-18 | GSE126727 | GEO
Project description:Background: Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered in transgenic petunia plants transformed with the CHS-A gene encoding chalcone synthase, in which nonpigmented sectors in flowers or completely white flowers are produced. Some of the flower-color patterns observed in transgenic petunias having CHS-A cosuppression resemble those in existing nontransgenic varieties. Although the mechanism by which white sectors are generated in nontransgenic petunia is known to be due to RNA silencing of the CHS-A gene as in cosuppression, whether the same trigger(s) and/or pattern of RNA degradation are involved in these phenomena has not been known. Here, we addressed this question using deep-sequencing and bioinformatic analyses of small RNAs. Results: We analyzed short interfering RNAs (siRNAs) produced in nonpigmented sectors of petal tissues in transgenic petunia plants that have CHS-A cosuppression and a nontransgenic petunia variety Red Star, that has naturally occurring CHS-A RNA silencing. In both silencing systems, 21-nt and 22-nt siRNAs were the most and the second-most abundant size classes, respectively. CHS-A siRNA production was confined to exon 2, indicating that RNA degradation through the RNA silencing pathway occurred in this exon. Common siRNAs were detected in cosuppression and naturally occurring RNA silencing, and their ranks based on the number of siRNAs in these plants were correlated with each other. Noticeably, highly abundant siRNAs were common in these systems. Phased siRNAs were detected in multiple phases at multiple sites, and some of the ends of the regions that produced phased siRNAs were conserved. Conclusions: The features of siRNA production found to be common to cosuppression and naturally occurring silencing of the CHS-A gene indicate mechanistic similarities between these silencing systems especially in the biosynthetic processes of siRNAs including cleavage of CHS-A transcripts and subsequent production of secondary siRNAs in exon 2. The data also suggest that these events occurred at multiple sites, which can be a feature of these silencing phenomena. Small RNAs isolated from petal tissues in two petunia lines were analyzed.
2013-12-14 | E-GEOD-42965 | biostudies-arrayexpress
Project description:affy_petaldvt_lyon_rose. The objective is to identify genes involved in petal development in rose. We aim at identifying genes whose expression correlates with flower opening and scent emission. In this study, we used a microarray approach to compare the transcriptome of a scented rose flower (PF) versus non-scented rose flower (RF). Samples (petal tissues) were collected at the same time early in the afternoon. Total RNA was extracted using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays. Keywords: scented vs non-scented flowers 4 arrays - rose. Scented and non-scented flowers, 2 replicates each.
2011-08-31 | E-GEOD-18357 | biostudies-arrayexpress
Project description:Plants perceive herbivory induced volatiles and respond to them by upregulating their defenses. So far, the organs responsible for volatile perception remain poorly described. Here, we show that responsiveness to the herbivory induced green leaf volatile (Z)-3-hexenyl acetate (HAC) in terms of volatile emission, transcriptional regulation and jasmonate defense hormone activation is largely constrained to younger maize leaves. Older leaves are much less sensitive to HAC. In a given leaf, responsiveness to HAC is high at immature developmental stages and drops off rapidly during maturation. Responsiveness to the non-volatile elicitor ZmPep3 shows an opposite pattern, demonstrating that this form of hyposmia (i.e. decreased sense of smell) is not due to a general defect in jasmonate defense signaling in mature leaves. Neither stomatal conductance nor leaf cuticle composition explain the unresponsiveness of older leaves to HAC, suggesting perception mechanisms upstream of jasmonate signaling as driving factors. Finally, we show that hyposmia in older leaves is not restricted to HAC, and extends to the full blend of herbivory induced volatiles. In conclusion, our work identifies immature maize leaves as dominant stress volatile sensing organs. The tight spatiotemporal control of volatile perception may facilitate within-plant defense signaling to protect young leaves, and may allow plants with complex architectures to explore the dynamic odor landscapes at the outer periphery of their shoots
2023-07-10 | GSE236332 | GEO
Project description:Background: Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered in transgenic petunia plants transformed with the CHS-A gene encoding chalcone synthase, in which nonpigmented sectors in flowers or completely white flowers are produced. Some of the flower-color patterns observed in transgenic petunias having CHS-A cosuppression resemble those in existing nontransgenic varieties. Although the mechanism by which white sectors are generated in nontransgenic petunia is known to be due to RNA silencing of the CHS-A gene as in cosuppression, whether the same trigger(s) and/or pattern of RNA degradation are involved in these phenomena has not been known. Here, we addressed this question using deep-sequencing and bioinformatic analyses of small RNAs. Results: We analyzed short interfering RNAs (siRNAs) produced in nonpigmented sectors of petal tissues in transgenic petunia plants that have CHS-A cosuppression and a nontransgenic petunia variety Red Star, that has naturally occurring CHS-A RNA silencing. In both silencing systems, 21-nt and 22-nt siRNAs were the most and the second-most abundant size classes, respectively. CHS-A siRNA production was confined to exon 2, indicating that RNA degradation through the RNA silencing pathway occurred in this exon. Common siRNAs were detected in cosuppression and naturally occurring RNA silencing, and their ranks based on the number of siRNAs in these plants were correlated with each other. Noticeably, highly abundant siRNAs were common in these systems. Phased siRNAs were detected in multiple phases at multiple sites, and some of the ends of the regions that produced phased siRNAs were conserved. Conclusions: The features of siRNA production found to be common to cosuppression and naturally occurring silencing of the CHS-A gene indicate mechanistic similarities between these silencing systems especially in the biosynthetic processes of siRNAs including cleavage of CHS-A transcripts and subsequent production of secondary siRNAs in exon 2. The data also suggest that these events occurred at multiple sites, which can be a feature of these silencing phenomena.
2013-12-14 | GSE42965 | GEO