Ontology highlight
ABSTRACT:
PROVIDER: PRJNA421316 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6353500_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR6353510_1.fastq.gz | Fastqsanger.gz | |||
| SRR6353510_2.fastq.gz | Fastqsanger.gz | |||
| SRR6353520.fastq.gz | Fastqsanger.gz | |||
| SRR6353530_1.fastq.gz | Fastqsanger.gz |
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Project description:Pathogen causing esca and grapevine declines
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Project description:Aims: Cancer is an important public health problem worldwide. In recent years, methods based on the analysis of plasma cfDNA which is as an emerging technology have been largely explored for noninvasive prenatal testing and cancer liquid biopsy. We inferred both epigenetic and genetic biomarkers of esophageal cancer (ESCA) in cfDNA with adapted SALP-seq. Materials & methods: Next Generation Sequencing libraries of cfDNA samples from ESCA patients and healthy people were constructed by using SALP-seq. We performed bioinformatics analysis on our sequencing data to find cancer-specific biomarkers. Results & conclusion: 54 important regulatory elements of ESCA, 49 epigenetic and 37 genetic ESCA-specific genes were inferred in cfDNA with SALP-seq, which may ultimately contribute to the development of effective diagnostic and therapeutic approaches for ESCA.
2022-08-28 | GSE136541 | GEO
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:Fomitiporia mediterranea (Fmed) is one of the main fungal species found in grapevine wood rot, also called “amadou”, one of the most typical symptoms of grapevine trunk disease Esca. This fungus is functionally classified as a white-rot, able to degrade all wood structure polymers, i.e., hemicelluloses, cellulose, and the most recalcitrant component, lignin. Specific enzymes are secreted by the fungus to degrade those components, namely carbohydrate active enzymes for hemicelluloses and cellulose, which can be highly specific for given polysaccharide, and peroxidases, which enable white-rot to degrade lignin, with specificities relating to lignin composition as well. Furthermore, besides polymers, a highly diverse set of metabolites often associated with antifungal activities is found in wood, this set differing among the various wood species. Wood decayers possess the ability to detoxify these specific extractives and this ability could reflect the adaptation of these fungi to their specific environment. The aim of this study is to better understand the molecular mechanisms used by Fmed to degrade wood structure, and in particular its potential adaptation to grapevine wood. To do so, Fmed was cultivated on sawdust from different origins: grapevine, beech, and spruce. Carbon mineralization rate, mass loss, wood structure polymers contents, targeted metabolites and secreted proteins were measured. We used the well-known white-rot model Trametes versicolor for comparison. Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture. Moreover, on both substrates, a simultaneous degradation pattern and the degradation of wood extractives were demonstrated, and proteomic analyses identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes. These results could explain at least partially the adaptation of Fmed to grapevine wood structural composition compared to other wood species and suggest that other biotic and abiotic factors should be considered to fully understand the potential adaptation of Fmed to its ecological niche.
2022-09-27 | PXD036889 | Pride
Project description:Transcriptional profiling of tumor tissues and normal tissues from ESCA.
2022-04-03 | GSE199967 | GEO
Project description:WRKY genes are transcription factors involved in plant response to pathogen attacks in many plant species. These proteins have been shown to activate expression of defence genes in a salicylic acid- and/or jasmonic acid-dependent signalling pathway. To understand the molecular mechanisms involved in grapevine defence, we previously identified a WRKY gene, VvWRKY1, which was able to enhance tolerance to fungal pathogens when overexpressed in tobacco. To elucidate its role in grapevine, we generated transgenic grapevines that overexpress VvWRKY1. Microarray analyses were performed to compare global gene expression in leaves of the transgenic and wild-type lines. Results showed that expression of genes encoding defence-related proteins was enhanced in the transgenic 35S::VvWRKY1 line. Quantitative RT-PCR analysis confirmed that three genes putatively involved in jasmonic acid signalling pathway, two genes encoding JASMONATE ZIM-domain (JAZ) proteins and one lipoxygenase, are over-expressed. The ability of VvWRKY1 to trans-activate their corresponding promoters was confirmed by transient expression assay in grape protoplasts. After challenging with the downy mildew pathogen Plasmopara viticola, resistance was enhanced in the transgenic line compared to the wild-type line. These results suggest that VvWRKY1 transcription factor is able to control plant disease resistance to one of the main grapevine pathogen by activating jasmonic acid signalling pathway in grapevine.
2012-12-19 | E-MTAB-1077 | biostudies-arrayexpress
Project description:Grapevine downy mildew is an important disease affecting crop production and causing severe losses. To identify genotype-dependent responses towards this pathogen and to explore the molecular mechanisms involved in grapevine-P. viticola resistance, we have conducted a proteomic analysis of leaf samples from resistant and susceptible grapevine genotypes prior and post-inoculation with the pathogen. Proteins were analyzed by quantitative two-dimensional differential gel electrophoresis (2D-DIGE). The analysis able to identified 50 unique proteins. Functional analysis showed that photosynthesis and metabolism were the main categories differentiating genotypes at 0h and that P. viticola-responsive proteins were mainly involved in photosynthesis, carbohydrate metabolism, stress and defense responses and redox homeostasis. ROS production, total antioxidant capacity and lipid peroxidation on both genotypes were determined and together with the proteome data suggest that Regent presents a strict balance between ROS control and signaling leading to plant cell death activation. Our data reveals the genotype-dependent modulation of plant metabolism and defense responses providing new insights into underlying molecular processes of grapevine resistance against the downy mildew fungus.
2016-12-24 | PXD002920 | Pride
Project description:Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features associated with resistance to the phytoplasma and/or possibly with its vector. In this work, RNA-Seq was used to compare early transcriptional changes occurring during the three-trophic interaction between the phytoplasma, its vector and the grapevine, represented by two different cultivars, one very susceptible to the disease and the other scarcely susceptible. Background: Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features associated with resistance to the phytoplasma and/or possibly with its vector. In this work, RNA-Seq was used to compare early transcriptional changes occurring during the three-trophic interaction between the phytoplasma, its vector and the grapevine, represented by two different cultivars, one very susceptible to the disease and the other scarcely susceptible. The comparison of the transcriptomic responses highlighted both passive and active defense mechanisms against the vector and/or the pathogen in the scarcely-susceptible variety, as well as the capacity of the phytoplasmas to repress the defense reaction against the insect in the susceptible variety.
2019-06-13 | E-MTAB-7710 | biostudies-arrayexpress