Caryophyllales
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA388222 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4162958_1.fastq.gz | Fastqsanger.gz | |||
| SRR4162958_2.fastq.gz | Fastqsanger.gz | |||
| SRR6787490_1.fastq.gz | Fastqsanger.gz | |||
| SRR6787490_2.fastq.gz | Fastqsanger.gz | |||
| SRR6787500_1.fastq.gz | Fastqsanger.gz |
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Project description:Stranded transcriptome sequencing from 14 species across the plant order Caryophyllales
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Project description:•Carnivorous plants from the order Caryophyllales co-opted plant phytohormones from the group of jasmonates for regulation of digestive enzyme activities. But not all genera of carnivorous plants are evenly explored and the digestive physiology of the Australian carnivorous rainbow plants of the genus Byblis (order: Lamiales) is only very poorly understood. •Here, we investigated the composition of digestive enzymes in the secreted fluid of Byblis filifolia using LC/MS, measured enzyme activities and analysed the phytohormone tissue level after experimental feeding on fruit flies and coronatine application. •Several hydrolytic digestive enzymes were identified in the secreted digestive fluid which were clearly upregulated in the presence of insect prey. But in contrast to sundew plant Drosera capensis, endogenous jasmonate did not accumulate and coronatine, a molecular mimic of jasmonates, was not able to trigger enzyme secretion. •Our results document that carnivorous plant B. filifolia is fully carnivorous with their own digestive enzyme repertoire. However in contrast to carnivorous genera from the order Caryophyllales, they are not under the control of jasmonates. This indicates that jasmonates have not been co-opted for regulation of digestive enzyme activity repeatedly during evolution of carnivorous plants.
2025-05-20 | PXD060459 | Pride
Project description:Stranded transcriptome sequencing of 17 species from the plant family Amaranthaceae s.l.
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Project description:C. elegans mutants deleted for TDP-1, an ortholog of the neurodegeneration-associated RNA binding protein TDP-43, display only mild phenotypes. Nevertheless, transcriptome sequencing revealed that many RNAs were altered in accumulation and/or processing in the mutant. Analysis of these transcriptional abnormalities demonstrates that a primary function of TDP-1 is to limit formation or stability of double-stranded RNA. Specifically, we found that deletion of tdp-1: 1) preferentially alters the accumulation of RNAs with inherent double stranded structure (dsRNA); 2) increases the accumulation of nuclear dsRNA foci, 3) enhances the frequency of adenosine-to-inosine RNA editing, and 4) dramatically increases the amount of transcripts immunoprecipitable with a dsRNA-specific antibody, including intronic sequences, RNAs with antisense overlap to another transcript, and transposons. We also show that TDP-43 knockdown in human cells results in accumulation of dsRNA , indicating that suppression of dsRNA is a conserved function of TDP-43 in mammals. Altered accumulation of structured RNA may account for some of the previously described molecular phenotypes (e.g., altered splicing) resulting from reduction of TDP-43 function. 24 samples: 3 tdp-1 polyA samples with 3 N2 controls, 3 tdp1J2 immunoprecipitated samples and tdp1 total RNA input with 3 N2 J2 immunoprecipitated controls (with N2 input), 3 tdp1 total RNA samples for RNA editing analysis with 3 N2 total RNA controls and an adr-2 mutant control, 2 tdp1 CHIPseq samples with RNAsecontrol.
2014-11-19 | E-GEOD-61581 | biostudies-arrayexpress
Project description:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. lyrata that allow for intra-specific transcriptome comparison in several major developmental stages. Please view also related dataset GSE69077 (RNA-sequencing of heat stressed A. lyrata and A. thaliana plants).
2015-08-01 | GSE69222 | GEO
Project description:C. elegans mutants deleted for TDP-1, an ortholog of the neurodegeneration-associated RNA binding protein TDP-43, display only mild phenotypes. Nevertheless, transcriptome sequencing revealed that many RNAs were altered in accumulation and/or processing in the mutant. Analysis of these transcriptional abnormalities demonstrates that a primary function of TDP-1 is to limit formation or stability of double-stranded RNA. Specifically, we found that deletion of tdp-1: 1) preferentially alters the accumulation of RNAs with inherent double stranded structure (dsRNA); 2) increases the accumulation of nuclear dsRNA foci, 3) enhances the frequency of adenosine-to-inosine RNA editing, and 4) dramatically increases the amount of transcripts immunoprecipitable with a dsRNA-specific antibody, including intronic sequences, RNAs with antisense overlap to another transcript, and transposons. We also show that TDP-43 knockdown in human cells results in accumulation of dsRNA , indicating that suppression of dsRNA is a conserved function of TDP-43 in mammals. Altered accumulation of structured RNA may account for some of the previously described molecular phenotypes (e.g., altered splicing) resulting from reduction of TDP-43 function.
2014-11-19 | GSE61581 | GEO
Project description:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. lyrata that allow for intra-specific transcriptome comparison in several major developmental stages. Arabidopsis lyrata and Arabidopsis thaliana aerial tissues were collected from mock treated plants, total RNA isolated and poly-A RNA populations sequenced
2015-08-01 | E-GEOD-69222 | biostudies-arrayexpress
Project description:Transcriptome sequencing of non-model organisms is valuable resource of the genetic basis of ecological-meaningful traits. The Royal Irises, Iris section Oncocyclus (Iris: Iridaceae, order Asparagales), are a Middle-East group of species in the course of speciation. The species are characterized with extremely large flowers, a huge range of flower colors and a unique pollination system. The Royal Irises, which are a symbol of conservation in the Middle-east, serve as a model for evolutionary processes of speciation and plant ecology. However, there are not sufficient transcriptomic and genomic data for molecular characterization. Thus, it is necessary to generate massive transcript sequences for functional characterization and molecular marker development for the Royal Irises. The Iris transcriptome sequencing provides valuable resource for studying adaptation-associated traits in this non-model plant. Although intensive eco-evolutionary studies, this is the first reported transcriptome for the Royal Irises. The data available from this study will facilitate gene discovery, functional genomic studies and development of molecular markers in irises, and will provide genetic tools for their conservation.
2021-08-18 | GSE121786 | GEO
Project description:Caryophyllales Transcriptome or Gene expression
| PRJNA269655 | ENA