Responses of Zea mays root tissue to inoculation with the necrotrophic root pathogen Phytophthora cinnamomi
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE27626 | GEO | 2011/03/02
SECONDARY ACCESSION(S): PRJNA138239
REPOSITORIES: GEO
Similar Datasets
Project description:Phytophthora cinnamomi is a devastating soil-borne oomycete with a very broad host range however there remains a major gap in the understanding of plant resistance responses to the pathogen, furthermore, necrotrophic plant-pathogen interactions, particularly those of root pathogens, remain poorly understood. Zea mays exhibits non-host resistance to the pathogen and has been well characterised as a model species. Using the maize Affymetrix GeneChip array we conducted genome-wide gene expression profiling to elucidate the defence genes and pathways which are induced in the root tissue of a resistant plant species to the pathogen. Each experimental repeat consisted of 60 Z. mays seedlings in total: 15 control and 15 inoculated plants per timepoint. Root tissue was harvested and snap frozen in liquid nitrogen and stored at -80°C until required. All harvested root tissue within each treatment group at each time point was pooled for total RNA extractions. Three technical repeats were conducted resulting in a total of 180 sampled plants and 12 samples of purified total RNA for microarray analysis. Total RNA was labelled, hybridised and scanned using standard Affymetrix protocols and resulted in 12 .CEL files. Raw data was processed using Partek Genomics Suite software and normalised using Robust Multi-Chip Average Software. Differentially expressed genes were defined by a fold difference of >1.5 (log2) and those with a P value cutoff of <0.05 were considered statistically significant.
2011-03-02 | E-GEOD-27626 | biostudies-arrayexpress
Project description:Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to particular physiological characteristics, no treatments against diseases caused by oomycetes are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. The present project is focused on the molecular mechanisms that underlie the compatible plant-oomycete interaction and plant disease.The laboratory developed a novel interaction system involving the model plant, Arabidopsis thaliana and Phytophthora parasitica, a soil-borne pathogen infecting a wide host range, thus representing the majority of Phytophthora species. A characteristic feature of the compatible Arabidopsis/Phytophthora parasitica interaction is an extended biotrophic phase, before infection becomes necrotrophic. Because the initial biotrophic phase is extremely short on natural (e.g. solanaceous) hosts, the Arabidopsis system provides the opportunity to analyze, for both interaction partners, the molecular events that determine the initiation of infection and the switch to necrotrophy.The present project aims at analyzing the compatible interaction between A. thaliana roots and Phytophthora parasitica. The Affymetrix A. thaliana full genome chip will be used to characterize modulations of the transcriptome occurring over a period of 24h from the onset of plant root infection to the beginning of necrotrophy. Parallel to this study, a custom designed Phytophthora parasitica biochip will enable analyzing of Phytophthora parasitica gene expression during the same stages. The pathosystem involving A. thaliana and Phytophthora parasitica was described in Attard A, Gourgues M, Callemeyn-Torre N, Keller H. 2010. The New phytologist 187: 449–460. The protocol for recovery of RNA from purified appressoria was described in Kebdani N, Pieuchot L, Deleury E, Panabieres F, Le Berre JY, Gourgues M. 2010. New Phytol 185: 248–257.
2014-03-01 | GSE51252 | GEO
Project description:Transcriptome response of avocado roots subjected to flooding, infection by the oomycete Phytophthora cinnamomi or a combination of both. Analysis was carried out at two time-points. Aim was to identify important genes in response to these stresses.
2017-02-14 | GSE81297 | GEO
Project description:Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to particular physiological characteristics, no treatments against diseases caused by oomycetes are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. The present project is focused on the molecular mechanisms that underlie the compatible plant-oomycete interaction and plant disease. The laboratory developed a novel interaction system involving the model plant, Arabidopsis thaliana, and Phytophthora parasitica, a soil-borne pathogen infecting a wide host range, thus representing the majority of Phytophthora species. A characteristic feature of the compatible Arabidopsis/P. parasitica interaction is an extended biotrophic phase, before infection becomes necrotrophic. Because the initial biotrophic phase is extremely short on natural (e.g. solanaceous) hosts, the Arabidopsis system provides the opportunity to analyze, for both interaction partners, the molecular events that determine the initiation of infection and the switch to necrotrophy. The present project aims at analyzing the compatible interaction between A. thaliana roots and P. parasitica. The Affymetrix A. thaliana full genome chip will be used to characterize modulations of the transcriptome occurring over a period of 24h from the onset of plant root infection to the beginning of necrotrophy. Parallel to this study, a custom-designed P. parasitica biochip will enable analyzing of P. parasitica gene expression during the same stages. 10 samples were used in this experiment.
2010-04-28 | E-GEOD-20226 | biostudies-arrayexpress
Project description:Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to particular physiological characteristics, no treatments against diseases caused by oomycetes are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. The present project is focused on the molecular mechanisms that underlie the compatible plant-oomycete interaction and plant disease. The laboratory developed a novel interaction system involving the model plant, Arabidopsis thaliana, and Phytophthora parasitica, a soil-borne pathogen infecting a wide host range, thus representing the majority of Phytophthora species. A characteristic feature of the compatible Arabidopsis/P. parasitica interaction is an extended biotrophic phase, before infection becomes necrotrophic. Because the initial biotrophic phase is extremely short on natural (e.g. solanaceous) hosts, the Arabidopsis system provides the opportunity to analyze, for both interaction partners, the molecular events that determine the initiation of infection and the switch to necrotrophy. The present project aims at analyzing the compatible interaction between A. thaliana roots and P. parasitica. The Affymetrix A. thaliana full genome chip will be used to characterize modulations of the transcriptome occurring over a period of 24h from the onset of plant root infection to the beginning of necrotrophy. Parallel to this study, a custom-designed P. parasitica biochip will enable analyzing of P. parasitica gene expression during the same stages.
2010-04-20 | GSE20226 | GEO
Project description:Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to particular physiological characteristics, no treatments against diseases caused by oomycetes are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. The present project is focused on the molecular mechanisms that underlie the compatible plant-oomycete interaction and plant disease.The laboratory developed a novel interaction system involving the model plant, Arabidopsis thaliana and Phytophthora parasitica, a soil-borne pathogen infecting a wide host range, thus representing the majority of Phytophthora species. A characteristic feature of the compatible Arabidopsis/Phytophthora parasitica interaction is an extended biotrophic phase, before infection becomes necrotrophic. Because the initial biotrophic phase is extremely short on natural (e.g. solanaceous) hosts, the Arabidopsis system provides the opportunity to analyze, for both interaction partners, the molecular events that determine the initiation of infection and the switch to necrotrophy.The present project aims at analyzing the compatible interaction between A. thaliana roots and Phytophthora parasitica. The Affymetrix A. thaliana full genome chip will be used to characterize modulations of the transcriptome occurring over a period of 24h from the onset of plant root infection to the beginning of necrotrophy. Parallel to this study, a custom designed Phytophthora parasitica biochip will enable analyzing of Phytophthora parasitica gene expression during the same stages. The pathosystem involving A. thaliana and Phytophthora parasitica was described in Attard A, Gourgues M, Callemeyn-Torre N, Keller H. 2010. The New phytologist 187: 449–460. The protocol for recovery of RNA from purified appressoria was described in Kebdani N, Pieuchot L, Deleury E, Panabieres F, Le Berre JY, Gourgues M. 2010. New Phytol 185: 248–257. A series of 14 hybridizations corresponding to two biological replicates each corresponding to RNA extractions of the following biological conditions were used: 1-Vegetative mycelium (recovered from two samples of 4 day-old cultures in liquid V8 medium at 24°C), 2- Motile zoospores (recovered from 8 independent cultures), 3-Appressoria differentiated on onion epidermis (epidermis from 20 onion bulbs inoculated with zoospores collected from 8 independent Petri dishes); appressoria collected 3 hours after inoculation (24 °C), 5- Infection of A. thaliana roots by Phytophthora parasitica zoospores (samples recovered at 2.5, 6, 10.5 and 30 hours post inoculation; 5 inoculated plants for each sample).
2014-03-01 | E-GEOD-51252 | biostudies-arrayexpress
Project description:The oomycete pathogen Phytophthora sojae causes root rot of soybean. During infection, the pathogen is thought to deliver dozens, if not hundreds, of effector proteins into the host to manipulate intracellular systems. Although these pathogen proteins often exhibit similar N-terminal delivery domains, the remaining effector region is rarely homologous to known protein domains, making it difficult to predict its biochemical function during infection. As a complement to studies in the natural host, Saccharomyces cerevisiae has been successfully used as a model system to explore the biochemical function of individual pathogen effectors. The presumption is that many effectors target conserved eukaryotic pathways in the host and consequently the expression of effectors in yeast will confer corresponding phenotypes. Indeed, putative effector functions identified using yeast functional genomic approaches have subsequently been validated in the natural host. Over-expression of the Phytophthora sojae effector Avh172 (PsAvh172) inhibits the growth of Saccharomyces cerevisiae, suggesting that the effector targets a biological pathway conserved with plants. In this study, the transcriptomes of yeast expressing PsAvh172 or an empty vector were compared to examine the global transcriptional response, in hopes of discerning the effectors biochemical target.
2021-01-01 | E-MTAB-4682 | biostudies-arrayexpress
Project description:The oomycete pathogen Phytophthora sojae causes root rot of soybean. During infection, the pathogen is thought to deliver dozens, if not hundreds, of effector proteins into the host to manipulate intracellular systems. Although these pathogen proteins often exhibit similar N-terminal delivery domains, the remaining effector region is rarely homologous to known protein domains, making it difficult to predict its biochemical function during infection. As a complement to studies in the natural host, Saccharomyces cerevisiae has been successfully used as a model system to explore the biochemical function of individual pathogen effectors. The presumption is that many effectors target conserved eukaryotic pathways in the host and consequently the expression of effectors in yeast will confer corresponding phenotypes. Indeed, putative effector functions identified using yeast functional genomic approaches have subsequently been validated in the natural host. Over-expression of the Phytophthora sojae effector Avh110 (PsAvh110) inhibits the growth of Saccharomyces cerevisiae, suggesting that the effector targets a biological pathway conserved with plants. In this study, the transcriptome of yeast expressing PsAvh110 or an empty vector were compared to examine the global transcriptional response, in hopes of discerning the effector's biochemical target.
2021-11-12 | E-MTAB-9566 | biostudies-arrayexpress
Project description:Phytophthora infestans is most notorious oomycete causing a devastating disease on tomato called late blight. The molecular mechanisms involved in host-parasite interaction is still unexplored well. Investigation of changes in gene expression profile after pathogen infection to find out the mechanisms involved in infection process
2011-10-25 | GSE33177 | GEO
Project description:Introduction: Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis. Methods: To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analysed the transcriptome of P. medicaginis across three phases of colonisation of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem. Results: The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterisation of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death. Discussion: These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase.
2024-08-05 | GSE183604 | GEO