Genomics of oomycete downy mildew plant pathogens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA396554 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR11844400_1.fastq.gz | Fastqsanger.gz | |||
| SRR11844400_2.fastq.gz | Fastqsanger.gz | |||
| SRR11844401_1.fastq.gz | Fastqsanger.gz | |||
| SRR11844401_2.fastq.gz | Fastqsanger.gz |
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Project description:Changes in gene expression form a crucial part of the plant response to pathogen infection. Whole-leaf expression profiling has played a valuable role in identifying genes and processes that contribute to the interactions between the model plant Arabidopsis thaliana and a diverse range of pathogens. However, for highly localised infections, such as downy mildew caused by the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis (Hpa), whole-leaf profiling may fail to capture the complete Arabidopsis response. Highly localised expression changes may be diluted by the comparative abundance of non-responding leaf cells or the Hpa oomycete evading detection by cells. Furthermore, local and systemic Hpa responses of a differing nature may become convoluted. To address this we applied the technique of Fluorescence Activated Cell Sorting (FACS), typically used for analyzing plant abiotic responses, to the study of plant-pathogen interactions. Using the promoter of Downy Mildew Resistant 6 (DMR6) linked to GFP as a fluorescent marker of pathogen-contacting cells, we isolated Hpa-proximal and Hpa-distal cells from infected leaf samples using FACS, and measured global gene expression.
2015-07-13 | GSE67100 | GEO
Project description:The downy mildew oomycete Hyaloperonospora arabidopsidis, an obligate filamentous pathogen, infect Arabidopsis by forming feeding structures called haustoria inside the host cell. Previous transcriptome analysis revealed host genes specifically induced during infection. However, whole infected tissue-derived RNA profiling may fail to capture the key transcriptional events that may occur exclusively in haustoriated host cells where the pathogen injects virulence effectors to modulate host immunity for successful accommodation. To understand the interaction between Arabidopsis and H. arabidopsidis at the cellular level, we established a new translating ribosome affinity purification (TRAP) system applicable to pathogen-responsive promoters, enabling haustoriated cell-specific RNA profiling. Among the host genes specifically expressed in H. arabidopsidis-haustoriated cells, we found genes that promote either susceptibility or resistance to the pathogen, providing new insights into the Arabidopsis/downy mildew interaction. We also expect that our new TRAP system could be applicable to several stimulus-specific contexts as well as other plant–pathogen interactions.
2022-12-25 | GSE220449 | GEO
Project description:Study of gene expression during Plasmopara viticola infection in the resistant Vitis vinifera cultivar 'Regent'. The oomycete fungus Plasmopara viticola (Berk. et Curt.) Berl. et de Toni is responsible for grapevine downy mildew disease. Most of the cultivated grapevines are sensitive to this pathogen, thus requiring intensive fungicide treatments. The molecular basis of resistance to this pathogen is poorly understood. We have carried out a cDNA microarray transcriptome analysis to identify grapevine genes associated with resistance traits. Early transcriptional changes associated with downy mildew infection in the resistant Vitis vinifera cultivar ‘Regent’, when compared to the susceptible cultivar ‘Trincadeira’, were analyzed. Transcript levels were measured at three time-points: 0, 6 and 12 hours post inoculation (hpi). Our data indicate that resistance in V. vinifera ‘Regent’ is induced after infection. This study provides the identification of several candidate genes that may be related to ‘Regent’ defense mechanisms, allowing a better understanding of this cultivar's resistance traits.
2012-04-06 | GSE28439 | GEO
Project description:Changes in gene expression form a crucial part of the plant response to pathogen infection. Whole-leaf expression profiling has played a valuable role in identifying genes and processes that contribute to the interactions between the model plant Arabidopsis thaliana and a diverse range of pathogens. However, for highly localised infections, such as downy mildew caused by the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis (Hpa), whole-leaf profiling may fail to capture the complete Arabidopsis response. Highly localised expression changes may be diluted by the comparative abundance of non-responding leaf cells or the Hpa oomycete evading detection by cells. Furthermore, local and systemic Hpa responses of a differing nature may become convoluted. To address this we applied the technique of Fluorescence Activated Cell Sorting (FACS), typically used for analyzing plant abiotic responses, to the study of plant-pathogen interactions. Using the promoter of Downy Mildew Resistant 6 (DMR6) linked to GFP as a fluorescent marker of pathogen-contacting cells, we isolated Hpa-proximal and Hpa-distal cells from infected leaf samples using FACS, and measured global gene expression. The whole experiment was carried out in triplicate, with two time points (5 and 7 days post-inoculation) and three cell types (pathogen-proximal, pathogen-distal and uninfected control), totalling 18 microarrays. Transgenic Arabidopsis thaliana Col-0 with the transgene pDMR6:GFP was used for all experiments. Seedling populations were inoculated with 30,000-60,000 spores/ml of Hyaloperonospora arabidopsis strain Noks1 at 7 days old, and overground tissue sampled at 5 and 7 days post-inoculation. Protoplasts were generated from these samples according to Grønlund et al. 2012 JOVE, and sorted by fluorescence activated cell sorting into a GFP-positive (pathogen-proximal) and GFP-negative (pathogen-distal) population. As a control, uninfected seedlings were also sampled at 12 and 14 days old (equivalent age of 5 and 7 days post-inoculation), protoplasts generated and sorted to yield a GFP-negative population of uninfected control cells. Gene expression was analysed using NimbleGen 12 x 135K microarrays, designed for the TAIR10 genome. Data was normalised using the Robust Multichip Averaging algorithm.
2015-07-13 | E-GEOD-67100 | biostudies-arrayexpress
Project description:A comparative proteomic analysis of grapevine leaves from the resistant genotype V. davidii ‘LiuBa-8’ (LB) and susceptible genotype V. vinifera ‘Pinot Noir’ (PN) at 12 hpi was conducted to understand the complex relationship between grapevine and P. viticola and the molecular mechanisms between difference resistant vitis genotypes at the early stage of infection. A total of 444 and 349 differentially expressed proteins (DEPs) were identified in LB and PN respectively at 12 hpi by iTRAQ. MapMan analysis showed that the majority of these DEPs were related to photosynthesis, metabolism, stress and redox. More up-expressed DEPs involved in photosynthesis and less down-expressed DEPs involved in metabolism contribute to the resistance in LB. PR10.2, PR10.3, HSF70.2 and HSP90.6 are proposed to be key proteins in both compatible and incompatible interactions. Accumulation H2O2 established the ROS signaling in incompatible interaction and APXs, GSTs maybe associated with the resistance of grapevine against downy mildew. Moreover, we verified four proteins to ensure the accuracy of proteome data using PRM. Overall, these data provide new insights into molecular events and provide valuable candidate proteins that could be used to illuminate molecular mechanisms underlying the incompatible and compatible interaction in early stage and eventually to be exploited to develop new protection strategy against downy mildew in grapevine.
2021-09-09 | PXD018845 | Pride
Project description:A comparative proteomic analysis of grapevine leaves from the resistant genotype V. davidii ‘LiuBa-8’ (LB) and susceptible genotype V. vinifera ‘Pinot Noir’ (PN) at 12 hpi was conducted to understand the complex relationship between grapevine and P. viticola and the molecular mechanisms between difference resistant vitis genotypes at the early stage of infection. A total of 444 and 349 differentially expressed proteins (DEPs) were identified in LB and PN respectively at 12 hpi by iTRAQ. MapMan analysis showed that the majority of these DEPs were related to photosynthesis, metabolism, stress and redox. More up-expressed DEPs involved in photosynthesis and less down-expressed DEPs involved in metabolism contribute to the resistance in LB. PR10.2, PR10.3, HSF70.2 and HSP90.6 are proposed to be key proteins in both compatible and incompatible interactions. Accumulation H2O2 established the ROS signaling in incompatible interaction and APXs, GSTs maybe associated with the resistance of grapevine against downy mildew. Moreover, we verified four proteins to ensure the accuracy of proteome data using PRM. Overall, these data provide new insights into molecular events and provide valuable candidate proteins that could be used to illuminate molecular mechanisms underlying the incompatible and compatible interaction in early stage and eventually to be exploited to develop new protection strategy against downy mildew in grapevine.
2021-09-09 | PXD018868 | Pride
Project description:Study of gene expression during Plasmopara viticola infection in the resistant Vitis vinifera cultivar 'Regent'. The oomycete fungus Plasmopara viticola (Berk. et Curt.) Berl. et de Toni is responsible for grapevine downy mildew disease. Most of the cultivated grapevines are sensitive to this pathogen, thus requiring intensive fungicide treatments. The molecular basis of resistance to this pathogen is poorly understood. We have carried out a cDNA microarray transcriptome analysis to identify grapevine genes associated with resistance traits. Early transcriptional changes associated with downy mildew infection in the resistant Vitis vinifera cultivar M-bM-^@M-^XRegentM-bM-^@M-^Y, when compared to the susceptible cultivar M-bM-^@M-^XTrincadeiraM-bM-^@M-^Y, were analyzed. Transcript levels were measured at three time-points: 0, 6 and 12 hours post inoculation (hpi). Our data indicate that resistance in V. vinifera M-bM-^@M-^XRegentM-bM-^@M-^Y is induced after infection. This study provides the identification of several candidate genes that may be related to M-bM-^@M-^XRegentM-bM-^@M-^Y defense mechanisms, allowing a better understanding of this cultivar's resistance traits. 3 time points: 0, 6 and 12 hours post inoculation by P. viticola. Two cultivars: control (Trinacedira) and test (Regent). Two biological replicates were performed at 0 hpi, and 3 biological replicates at 6 and 12hpi. At 12hpi, three technical replicates also were performed.
2012-04-05 | E-GEOD-28439 | biostudies-arrayexpress
Project description:Grapevine downy mildew caused by the Oomycete Plasmopara viticola is one of the most important diseases affecting Vitis spp. However, all cultivated European grapevine varieties are susceptible to P. viticola and the resistance needs to be introduced from other Vitaceae. Segregating populations derived from Muscadinia rotundifolia, a species closely related to Vitis, lead to the identification and mapping of two resistance genes, named Rpv1 and Rpv2. The macroscopic phenotypes of the resistance mediated by the two loci are different. Rpv2 plants completely inhibit P. viticola sporulation and produce very small necrotic lesions. In contrast, Rpv1 plants allow a rather limited but visible sporulation of P. viticola. The aim of the study is to understand the gene expression changes associated with downy mildew resistance mediated by these two loci. Gene expression patterns after P. viticola inoculation or mock inoculation are compared in incompatible (resistant plants bearing Rpv1 or Rpv2 locus) and compatible (susceptible plants with no resistance loci) interactions, using the Vitis vinifera GeneChip from Affymetrix. In order to limit the effect of the genetic background, the plant material consists in three pools of genotypes called B, C and D, respectively corresponding to partially resistant plants (Rpv1+/Rpv2-), totally resistant plants (Rpv1-/Rpv2+), and susceptible plants (Rpv1-/Rpv2-) derived from a segregating population. Each pool consists in 3 different genotypes. Plant leaf discs were inoculated with P. viticola sporangium suspension (i) or mock-inoculated with water (ni) and analysed 6 hours post-inoculation. For each experimental condition, we performed two biological replicates. Experiment Overall Design: 3 plant genotypes were analyzed: Rpv1+/Rpv2- (B), Rpv1-/Rpv2+ (C), and Rpv1-/Rpv2- (D). Plants were either inoculated with P. viticola (i) or mock-inoculated with water (ni). Biological replicates were performed for each experimental condition.
2009-07-01 | E-GEOD-11857 | biostudies-arrayexpress
Project description:Grapevine downy mildew caused by the Oomycete Plasmopara viticola is one of the most important diseases affecting Vitis spp. However, all cultivated European grapevine varieties are susceptible to P. viticola and the resistance needs to be introduced from other Vitaceae. Segregating populations derived from Muscadinia rotundifolia, a species closely related to Vitis, lead to the identification and mapping of two resistance genes, named Rpv1 and Rpv2. The macroscopic phenotypes of the resistance mediated by the two loci are different. Rpv2 plants completely inhibit P. viticola sporulation and produce very small necrotic lesions. In contrast, Rpv1 plants allow a rather limited but visible sporulation of P. viticola. The aim of the study is to understand the gene expression changes associated with downy mildew resistance mediated by these two loci. Gene expression patterns after P. viticola inoculation or mock inoculation are compared in incompatible (resistant plants bearing Rpv1 or Rpv2 locus) and compatible (susceptible plants with no resistance loci) interactions, using the Vitis vinifera GeneChip from Affymetrix. In order to limit the effect of the genetic background, the plant material consists in three pools of genotypes called B, C and D, respectively corresponding to partially resistant plants (Rpv1+/Rpv2-), totally resistant plants (Rpv1-/Rpv2+), and susceptible plants (Rpv1-/Rpv2-) derived from a segregating population. Each pool consists in 3 different genotypes. Plant leaf discs were inoculated with P. viticola sporangium suspension (i) or mock-inoculated with water (ni) and analysed 6 hours post-inoculation. For each experimental condition, we performed two biological replicates. Keywords: normal vs disease comparison
2009-06-20 | GSE11857 | GEO
Project description:Here we report on the identification of Arabidopsis genes that are induced during compatible but not during incompatible interactions with the downy mildew pathogen Hyaloperonospora arabidopsidis. This set of so-called compatible specific (CS) genes contrasts the large group of defence-associated genes that is differentially expressed during both compatible and incompatible interactions. From the 17 identified CS-genes, 6 belong to the ERF family of transcription factor genes, suggesting that these ERFs have a role during compatibility. The majority of CS-genes are differentially regulated in response to various forms of abiotic stress. In silico analysis of the CS-genes revealed an over-representation of DREB1A/CBF3 binding sites and EveningElement motifs in their promoter regions. The CS-ERFs are closely related to the CBF transcription factors and could potentially bind the DREB1A/CBF3 promoter elements in the CS-genes. Transcript levels of CS-genes peak at 2-3 days post inoculation, when pathogen growth is highest, and decline at later stages of infection. The induction of several CS-genes was found to be isolate-dependant. This suggests that the identified CS-genes could be the direct or indirect targets of downy mildew effector proteins that promote disease susceptibility.
2009-06-10 | GSE14946 | GEO