Ontology highlight
ABSTRACT:
PROVIDER: PRJNA899094 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22221700_1.fastq.gz | Fastqsanger.gz | |||
| SRR22221700_2.fastq.gz | Fastqsanger.gz | |||
| SRR22221701_1.fastq.gz | Fastqsanger.gz | |||
| SRR22221701_2.fastq.gz | Fastqsanger.gz | |||
| SRR22221702_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 384 |
Similar Datasets
Project description:In this study we functionally characterized the grapevine VviNAC33 by its transient and stable overexpression in grapevine homologous system and the creation of its chimeric repressor. Through the application of DAP-seq approach we identified putative direct targets of VviNAC33, among which the SGR1 involved in the breakdown of chlorophyll. Stable VviNAC33 overexpressing transgenic plants displayed an obvious degreening effect on leaves and an inhibition of leaf growth. Consistently, transgenic plant expressing a chimeric repressor of the VviNAC33 showed the opposite phenotypic alterations. Our results evidenced that VviNAC33 is a direct player of leaf senescence program and propose a blueprint of the complex transcriptional regulatory network that govern organ phase transition in grapevine. transcription factor VviNAC33 is directly involved in leaf degreening and organ growth.
2021-07-07 | GSE155445 | GEO
Project description:Grapevine red blotch is a recently identified viral disease that was first recognized in the Napa Valley of California. Infected plants showed foliar symptoms similar to leafroll, another grapevine viral disease, on vines testing negative for known grapevine leafroll-associated virus. Later, the Grapevine red blotch virus (GRBV) was independently discovered in the US states of California and New York and was demonstrated to be the causal agent of red blotch disease. Due to its wide occurrence in the US, vector transmission and impacts on grape industry, this virus has the potential to cause serious economic losses. Despite numerous attempts, it was not possible to isolate or visualize viral particles from GRBV infected plants. Consequently, this has hampered the development of a serological assay that would facilitate GRBV detection in grapevine. We therefore decided to explore mass spectrometry approaches in order to quantify GRBV in infected plants and to identify potential biomarkers for viral infection. We present for the first time the physical detection on the protein level of the two GRBV genes V1 (coat protein) and V2 in grapevine tissue lysates. The GRBV coat protein load in leaf petioles was determined to be in the range of 100 to 900 million copies per milligram wet weight by using three heavy isotope labeled reference peptides as internal standards. The V1 copy number per unit wet tissue weight in leaves appeared to be about six times lower, and about 200-times lower in terms of protein concentration in the extractable protein mass than in petioles. We found a consistent upregulation of several enzymes involved in flavonoid biosynthesis in leaf and petiole extracts of GRBV-infected plants by label-free shotgun proteomics, indicating the activation of a defense mechanism against GRBV, a plant response already described for grapevine leafroll associated virus infection on the transcriptome level. Last but not least, we identified some other microorganisms belonging to the grapevine leaf microbiota, two bacterial species (Novosphingobium sp. Rr 2-17 and Methylobacterium) and one virus, Grapevine rupestris stem pitting associated virus.
2018-12-19 | PXD011002 | Pride
Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from grapevine wood infected by a fungal pathogen in the presence of a root biological control agent. One of the goals was to obtain molecular data about the fungus pathogen (Phaeomoniella chlamydospora) during grapevine wood infection. Grapevine pathogen-infected wood mRNA profiles of 2-month-old plantlets (14 days post infection) were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed by TopHat followed by Cufflinks. qRTaPCR validation was performed using SYBR Green assays. Using an optimized data analysis workflow, we mapped sequence reads to the grapevine genome (build IGGP 12x) and identified pathogen transcripts. RNAseq analyses, using a ribosomal RNA depletion technology for library preparation, provided identification of genes expressed by P. chlamydospora during infection: as for genes related to effector biosynthesis enzymes, carbohydrate-active enzymes and transcription regulators involved in known regulation pathways in fungi. Insights about P. oligandrum modulation of grapevine infection by this pathogen were also found. Our study represents the first detailed analysis of grapevine wood infection by a fungal pathogen generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive evaluation of mRNA content within grapevine wood tissue. We conclude that RNA-seq based transcriptome characterization would permit the dissection of complex biologic interactions.
2015-10-23 | E-MTAB-3966 | biostudies-arrayexpress
Project description:In this study we demonstrated that the grapevine NAC transcription factor VviNAC33 is directly involved in leaf degreening and organ growth. Through the application of DAP-seq approach we identified several putative targets of VviNAC33, among which the SGR1 involved in the breakdown of chlorophyll. Stable VviNAC33 overexpressing transgenic plants displayed an obvious degreening effect on leaves and an inhibition of leaf growth. Consistently, transgenic plant expressing a chimeric repressor of the VviNAC33 showed the opposite phenotypic alterations. Our results evidenced that VviNAC33 is a direct player of leaf senescence program and propose a blueprint of the complex transcriptional regulatory network that govern organ phase transition in grapevine.
2021-07-07 | GSE155037 | GEO
Project description:In this study, we demonstrated that the grapevine NAC transcription factor VviNAC33 is directly involved in leaf degreening and organ growth. Through the application of DAP-seq approach we identified several putative targets of VviNAC33, among which the SGR1 involved in the breakdown of chlorophyll. Stable VviNAC33 overexpressing transgenic plants displayed an obvious degreening effect on leaves and an inhibition of leaf growth. Consistently, transgenic plant expressing a chimeric repressor of the VviNAC33 showed the opposite phenotypic alterations. Our results evidenced that VviNAC33 is a direct player of leaf senescence program and propose a blueprint of the complex transcriptional regulatory network that govern organ phase transition in grapevine.
2021-07-07 | GSE156105 | GEO
Project description:Transcriptional profiling of Vitis vinifera cv. Chardonnay healthy vs. Phytoplasma-infected plants (Bois noir phytoplasma). Study was conducted on grapevine plants grown in the same vineyard (leaf midribs were sampled). Keywords: disease state analysis
2008-03-21 | GSE10906 | GEO
Project description:Characterization of proteins critical to fungal cellulosome assembly for Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis (cellulosomes are multi-protein complexes that tether plant biomass degrading enzymes together). These findings suggest that the fungal cellulosome is an independently evolved fungal complex that co-opted useful activities from bacterial neighbors within the herbivore rumen microbiome.
2018-10-19 | PXD006325 | Pride
Project description:Bacterial and fungal communities on grapevine leaves
| PRJNA237062 | ENA
Project description:The Lobaria pulmonaria holobiont consists of algal, fungal, cyanobacterial, and integrated diverse bacterial components and thrives in undisturbed, humid forests. We set out to investigate the role of the microbiome of L. pulmonaria in the adaptation of this ecologically sensitive lichen species to diverse climatic conditions. Our central hypothesis posited that microbiome composition and functionality aligns with continental-scale climatic parameters related to temperature and precipitation. In addition, we tested whether short-term weather dynamics, sampling season, and the genotypes of the fungal and algal partners influenced the variation in the lichen microbiome. Insights into compositional and functional changes within the microbiome were obtained using metaproteomics. Comparative examinations between Sub-Atlantic Lowland (SAL) and Alpine (ALP) regions unveiled the distinct impact of climate on microbiome functions.
2024-07-03 | PXD049079 | Pride
Project description:In this study we have analysed the regulation of miRNA in bone marrow derived macrophages in response to the fungal pathogen heat killed Candida albicans and bacterial cell wall component, LPS. The aim of the study was to identify and validate miRNAs involved in the innate immune system in response to fungal and bacterial stimuli and investigate potential mechanisms for their transcription.
2010-12-31 | GSE21970 | GEO