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E-MTAB-3966

ABSTRACT: Transcription profiling by high throughput sequencing of grapevine wood infected by a fungal pathogen in the presence of a root biological control agent

PROVIDER: E-MTAB-3966 | ExpressionAtlas | 2019-05-14

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-3966-analysis-methods.tsv	Tabular
	E-MTAB-3966-analytics.tsv	Tabular
	E-MTAB-3966-analytics.tsv.undecorated	Tabular
	E-MTAB-3966-analytics.tsv.undecorated.unrounded	Tabular
	E-MTAB-3966-analytics.tsv.unrounded	Tabular

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Next Generation Sequencing of grapevine wood pathogen infection in the presence of a root biocontrol agent.

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

Gene expression during wood pathogen infection in the presence of a root biocontrol agent in grapevine.

Project description:Transcriptional changes occurring at the infection site of 2 weeks old Cabernet sauvignon grapevine cuttings infected with a wood pathogen (Phaeomoniella chlamydospora) in the presence of a root-inoculated biocontrol agent (Pythium oligandrum). Gene expression profiling was done using the Nimblegen whole genome array with 3 biological replicates of 3 pooled wood chunks harvested 0 and 14 d after treatment (pathogen infection, biocontrol agent inoculation, mock treatment).

2016-03-15 | E-MTAB-3899 | biostudies-arrayexpress

E-MTAB-4350

Project description:Transcription profiling by high throughput sequencing in Ten Different Grapevine Cultivars

2016-02-02 | E-MTAB-4350 | ExpressionAtlas

E-MTAB-4278

Project description:Transcription profiling by high throughput sequencing of berries from grapevine cultivar Tannat

2020-06-22 | E-MTAB-4278 | ExpressionAtlas

E-GEOD-58653

Project description:Transcription profiling by high throughput sequencing of grapevine plants inoculated with Neofusicoccum parvum

2016-04-06 | E-GEOD-58653 | ExpressionAtlas

E-MTAB-4220

Project description:Transcription profiling by high throughput sequencing of grapevine Corvina cultivar during berry development

2016-04-07 | E-MTAB-4220 | ExpressionAtlas

E-GEOD-74428

Project description:Transcription profiling by high throughput sequencing of grapevine leaves at four different developmental stages

2016-10-17 | E-GEOD-74428 | ExpressionAtlas

E-MTAB-4811

Project description:Transcription profiling by high throughput sequencing of Zika virus-infected human brain organoids

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Whole-transcriptome microarray analysis of grapevine-Botrytis cinerea interaction during latent infection of berries (“noble rot”)

Project description:Purpose: Microarray technologies provide a unique opportunity to deeply investigate the molecular mechanisms involved in plant-pathogen interaction. Botrytis cinerea, is the agent of grapevine grey mould, but in yet uncharacterized environmental conditions, a latent infection can occur determining favourable metabolic and physico-chemical berry modifications which possibly contribute to the typical aromas of “passito” wines (“noble rot”). The present project aims at the identification of the grapevine responses to B. cinerea during fungal colonization in the latent form, in comparison with control berries. Methods: A total of 150 untreated berries were sampled as time 0 of the experiment. Moreover, 300 healthy berries have been artificially inoculated one by one with B. cinerea by injecting conidia under berry skin, in controlled conditions, reproducing an early stage (T1) and a late stage (T2) of noble rot pourri plein. Control samples (300 berries) have been inoculated with water and sampled at the same time of infected berries. The microarray experiments on T0 and healthy or infected samples in biological triplicate resulted in 15 samples to be analyzed (Agilent-048771 4x44K Grape all custom microarray chip; Agilent Technologies, Santa Clara, CA, USA). Conclusions: This work identified important molecular mechanisms involved in Botrytis cinerea colonization of grapevine berries during the noble rot infection.

2019-07-26 | GSE116740 | GEO

Next Generation Sequencing of grapevine wood pathogen infection in the presence of a root biocontrol agent.

Project description:Next Generation Sequencing of grapevine wood pathogen infection in the presence of a root biocontrol agent.

| PRJEB11405 | ENA