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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of the molecular dialogue between Botrytis cinerea and Vitis vinifera reveals a clear shift in defence mechanisms during berry ripening.

ABSTRACT: Full transcriptomes of the Botrytis cinerea wild-type strain B0510 inoculated on mature grapevine berries (Marselan cultivar) at 16h, 24h, 48h, and in vitro were compared to identify B. cinerea genes diffentially expressed during the infection stages. Grapevine berries were inoculated with Botrytis cinerea conidia and samples were taken at 16h, 24h and 48 hours post-inoculation. An additional control sample corresponding to mycelium growing on static liquid minimal medium was included in the experimental design in order to identify genes that would be differentially expressed between in vitro and in planta growth conditions. 3-4 replicates were performed. The 13 total-RNA samples were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

ORGANISM(S): Botrytis cinerea B05.10

SUBMITTER: Adeline SIMON

PROVIDER: E-GEOD-65559 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of the molecular dialogue between Botrytis cinerea and Vitis vinifera reveals a clear shift in defence mechanisms during berry ripening.

Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 inoculated on mature grapevine berries (Marselan cultivar) at 16h, 24h, 48h, and in vitro were compared to identify B. cinerea genes diffentially expressed during the infection stages.

2015-08-10 | GSE65559 | GEO

Analysis of the molecular dialogue between gray mold (Botrytis cinerea) and grapevine (Vitis vinifera) reveals a clear shift in defense mechanisms during berry ripening

Project description:Mature grapevine berries at the harvesting stage (MB) are very susceptible to the gray mold fungus Botrytis cinerea while veraison berries (VB) are not. We conducted simultaneous microscopic and transcriptomic analyses of the pathogen and the host to investigate the infectious process developed by B. cinerea on MB versus VB, and the plant defense mechanisms deployed to stop the fungus development. On the pathogen side, our genome-wide transcriptomic data revealed that B. cinerea genes up-regulated during infection of MB are enriched in functional categories related to necrotrophy such as degradation of plant cell wall, proteolysis, membrane transport, reactive oxygen species generation and detoxification. Quantitative-PCR on a set of representative genes related to virulence and microscopic observations further demonstrated that the infection is also initiated on VB but stops at the penetration stage. On the plant side, genome-wide transcriptomic analysis and metabolic data revealed a defense pathways switch during berry ripening. In response to B. cinerea infection, VB activated a burst of reactive oxygen species (ROS), the salicylate (SA)-dependent defense pathway, the synthesis of the resveratrol phytoalexin and cell-wall strengthening. In opposite, infected MB activated the jasmonate (JA)-dependent pathway which does not stop the fungal necrotrophic process. Grapevine berries at veraison (VB) and harvesting stages (MB) were inoculated with Botrytis cinerea B05-10 and samples were taken at 24h and 48h post-inoculation. An additional uninfected control sample taken at 0h post-inoculation was included in the experimental design. 3 replicates per sample were performed. The total-RNA samples were labeled and used for hybridization on NimbleGen 12plex Vitis vinifera gene expression array.

2015-08-08 | E-GEOD-65969 | biostudies-arrayexpress

RNA-Seq data of Vitis vinifera cv. Furmint berry samples (Tokaj wine region) exposed to noble rot

Project description:White grape (Vitis vinifera cv. Furmint) berry samples subjected to natural noble rot were collected in a vineyard in Mád, Hungary (Tokaj wine region). Raw data include grapevine and Botrytis cinerea sequence reads.

2021-11-25 | E-MTAB-11205 | biostudies-arrayexpress

Light and BcLTF1-dependent gene expression profiles in the phytopathogenic fungus Botrytis cinerea

Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutant deltaBcLTF1, cultured in continuous darkness or submitted to a light stimulation, were compared to identify light- or/and BcLTF1-dependent genes. The Botrytis cinerea wild-type strain and the null-mutant deltaBcLTF1 were cultured for 52h in continuous darkness ; then, cultures were exposed for 60 min to light before harvest (L) or were harvested after additional 60 min darkness (D). 4 replicates were performed. The 16 total-RNA samples (4 conditions* 4 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

2013-09-27 | E-GEOD-51192 | biostudies-arrayexpress

The VELVET complex in the gray mold fungus Botrytis cinerea: impact of BcLAE1 on differentiation, secondary metabolism and virulence

Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutants deltaBcVEL1 and deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays , were compared to identify BcVEL1 or/and BcLAE1-dependent genes. The Botrytis cinerea wild-type strain and the null-mutants deltaBcVEL1 and BcLAE1 were cultured for 48h onto solid grape juice medium with cellophane overlays. 4 replicates were performed. The 12 total-RNA samples (3 strains* 4 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

2015-02-01 | E-GEOD-63021 | biostudies-arrayexpress

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

Transcript and metabolite analysis of Vitis vinifera cv. Trincadeira berries infected with Botrytis cinerea reveals an activation of a non-sustained plant defense response

Project description:Vitis vinifera berries are sensitive towards infection by the necrothopic pathogen Botrytis cinerea leading to important economic losses worldwide. The combined analysis of the transcriptome and metabolome associated with the infection has not been previously performed in grapes or in another fleshy fruit. In an attempt to identify the molecular and metabolic mechanisms associated with the infection, pepper- corn size fruits (EL 29) were infected in-field and green berries (EL 33) and veraison berries (EL 35) were collected for microarray analysis complemented with metabolic profiling using GC-EI-TOF/MS and headspace GC-EI-MS platforms. The results provide evidence of a reprogramming of carbohydrate and lipid metabolisms towards increased synthesis of secondary metabolites involved in plant defense such as trans-resveratrol and gallic acid. The response is mainly activated in green berries with the putative involvement of jasmonic acid, ethylene, polyamines and auxins whereas salicylic acid does not seem to be involved. At veraison, however, genes encoding protein kinases, MYB and WRKY transcription factors, pathogenesis-related proteins, glutathione S-transferase, stilbene synthase and phenylalanine ammonia-lyase are no longer up-regulated or even down-regulated suggesting that the basal defense response is not active with the onset of ripening. This non-sustained defense response has not been previously reported for necrotrophic, biotrophic, or hemibiotrophic pathogens, and highlights the importance of conducting studies in fruits and not solely in vegetative tissues. Furthermore, this study provided with metabolic biomarkers of infection namely azelaic acid, arabitol and gluconic acid that can be used to monitor infection early in the vineyard. 2 time points in 2011 season at EL 33 and EL 35. 3 biological replicates. Grapes Infected with Botrytis cinerea and control with phosphate buffer

2014-03-31 | E-GEOD-52586 | biostudies-arrayexpress

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

Project description:Purpose: High throughput sequencing 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 genes deployed by B. cinerea during grape berries colonization in the latent form, in comparison with the saprophytic growth in vitro. Methods: A total of 300 healthy berries have been artificially inoculated one by one with B. cinerea by injecting conidia under berry skin, in controlled conditions, reproducing the pourri plein stage of noble rot. Control samples (300 berries) have been inoculated with water. The saprophytic growth was obtained in liquid nutrient medium in laboratory flasks, and the mycelium collected by filtration. The RNA-sequencing experiments on healthy or infected samples in biological triplicate resulted in 27 data sets to be analyzed (Illumina NextSeq500 paired-end sequencing; 533.779.730 total reads, 150 Gb of data). Conclusions: This work identified important molecular mechanisms involved in Botrytis cinerea colonization of grapevine berries during the noble rot infection.

2019-07-26 | GSE116274 | GEO

Phosphoproteome profiles of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea

Project description:This study describes the gel-free phosphoproteomic analysis the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea grown in vitro under non-limiting conditions.

2014-06-09 | PXD000817 | Pride

WRKY33-dependent expression of Arabidopsis genes upon Botrytis cinerea 2100 inoculation

Project description:The Arabidopsis thaliana mutant wrky33 is highly susceptible to the necrotrophic fungus Botrytis cinerea. Comparing the expression profiles of B. cinerea-infected wrky33 and WT plants we identified 2765 differentially expressed genes dependent on WRKY33, of which 1675 were up-regulated in the mutant (termed WRKY33-repressed genes) and 1090 were down-regulated in the mutant. Combined with ChIP-seq data 318 genes were identified as direct functional targets of WRKY33 at 14 h post inoculation with spores of Botrytis cinerea 2100. Comparison of altered gene expression in Arabidopsis WT and wrky33 mutant plants 14 hours post inoculation with Botrytis cinerea 2100.

2015-06-15 | E-GEOD-66290 | biostudies-arrayexpress

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