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RNA-seq-based analysis of the pathogen-induced defense transcriptome in Arabidopsis

ABSTRACT: Pathogen infection triggers transcriptional reprogramming in host plants, however we still know little about the dynamics of the pathogen-induced defense transcriptome. The goal of this study was to investigate the dynamic reprogramming of the defense transcriptome in response to Fusarium oxysporum infection in Arabidopsis using RNA-seq technology and to provide a comprehensive analysis of genes underlying the innate immune response against the fungal pathogen. Our results suggest that the Arabidopsis transcriptome is reprogrammed to co-ordinately express multiple positive and negative regulators following pathogen infection to modulate defense gene expression and disease resistance. Our study identified a number of novel genes responsive to pathogen infection and provided a rich source of pathogen responsive genes for further functional characterization.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE34241 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA149771

REPOSITORIES: GEO

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RNA-seq-based analysis of the pathogen-induced defense transcriptome in Arabidopsis

Project description:Pathogen infection triggers transcriptional reprogramming in host plants, however we still know little about the dynamics of the pathogen-induced defense transcriptome. The goal of this study was to investigate the dynamic reprogramming of the defense transcriptome in response to Fusarium oxysporum infection in Arabidopsis using RNA-seq technology and to provide a comprehensive analysis of genes underlying the innate immune response against the fungal pathogen. Our results suggest that the Arabidopsis transcriptome is reprogrammed to co-ordinately express multiple positive and negative regulators following pathogen infection to modulate defense gene expression and disease resistance. Our study identified a number of novel genes responsive to pathogen infection and provided a rich source of pathogen responsive genes for further functional characterization. Four samples (M1DPI, M6DPI, F1DPI and F6DPI; M=mock treated; F=Fusarium oxysporum infected; DPI=day post inoculation) were sequenced to identify pathogen responsive genes in each time point. Each sample was sequenced once, i.e. without biological replicate.

2012-06-01 | E-GEOD-34241 | biostudies-arrayexpress

Expression profiling of Fusarium oxysporum infected wild-type Arabidopsis and a 35S Fusarium SIX4 overexpression line.

2016-05-31 | GSE75928 | GEO

Expression profiling of Fusarium oxysporum infected wild-type Arabidopsis and a 35S Fusarium SIX4 overexpression line.

Project description:Fungal effectors play important roles in inciting disease development on host plants. We identified an effector (Secreted in Xylem4, SIX4) in an Arabidopsis infecting isolate (Fo5176) of the root-infecting fungal pathogen Fusarium oxysporum and demonstrated this effector is required for full virulence. To explore the role of Fo5176_SIX4 we use whole transcriptome profiling of root tissues from plants overexpressing this effector (35sSIX4) versus wild-type (Col-0) plants after F. oxysporum infection. We grew both WT and 35sSIX4 plants for four weeks in soil. After four weeks the plants were infected with Fusarium oxyporum isolate Fo5176, trays covered with a plastic dome and incubated at 28C. There were four independent replicates of each treatment and each replicate contained root tissue from 20 plants. Each replicate (8 in total) was harvested 4 days post inoculation and the resulting RNA was used for hybridization to an Affymetrix ATH1 chip.

2016-05-31 | E-GEOD-75928 | biostudies-arrayexpress

Expression profiling of wild-type Arabidopsis and an activation-tagged jaz7-1D line.

Project description:Jasmonate (JA) signaling plays a key role in mediating both resistance and susceptibility to the root-infecting fungal pathogen Fusarium oxysporum. Within this system, the roles of the JA-signaling repressor gene family of JASMONATE ZIM-domain (JAZ) genes had not been investigated. By screening JAZ T DNA insertion lines for altered resistance or susceptibility to F. oxysporum, we identified a JAZ7 mutant (jaz7-1D) highly susceptible to F. oxysporum infection. Further analyses revealed jaz7-1D exhibits constitutively active JAZ7 expression, enhanced expression of JA-defense marker genes, and increased sensitivity to JA-inhibition of root elongation. To further explore altered JA-signaling and JA-responses in this mutant, we use whole transcriptome profiling of jaz7-1D versus wild-type (Col-0) plants after mock/control and JA treatment.

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Transcriptome analysis reveals the response mechanism of Frl-mediated resistance to Fusarium oxysporum f. sp. radicis-lycopersici (FORL) infection in tomato

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Role of fungal cellulases upon plant infection

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Vanilla planifolia Jacks., transcriptomic response towards Fusarium oxysporum f. sp. vanillae infection

Project description:Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae. This pathogen causes root and stem rot in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with F. oxysporum f. sp. vanillae, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection. Analysis of global gene expression profiles indicated that the major transcriptional change occurred at 2 dpi, in comparison to 10 dpi. Whereas 3420 genes were found with a differential expression at 2 dpi, only 839 were identified at 10 dpi. The analysis of the transcriptional profile at 2 dpi suggests that, among other responses, vanilla plants prepare to counter the infection by gathering a pool of translational regulation-related transcripts. The screening of transcriptional changes of V. planifolia Jacks upon infection by F. oxysporum f. sp. vanillae provides insights into the plant molecular response, particularly the upregulation of ribosomal proteins at early stages. Thus, we propose that the plant-pathogen interaction between V. planifolia Jacks and F. oxysporum f. sp. vanillae causes a transcriptional reprogramming coupled with a translational regulation. Altogether, this study provides the identification of molecular players that could help to fight the most damaging disease of vanilla.

2019-11-19 | GSE134155 | GEO

Expression profiling of the Arabidopsis Mediator complex mutant pft1/med25 and wildtype infected with Fusarium oxysporum

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Transcription profiling of Arabidopsis Mediator complex mutant pft1/med25 and wildtype infected with Fusarium oxysporum

Project description:The Mediator complex is an evolutionary conserved multiprotein complex that plays an essential role in initiating and regulating transcription. Its function is to act as a universal adaptor between RNA Polymerase II and DNA-bound transcription factors to translate regulatory information from activators and repressors to the transcriptional machinery. We have found that the PFT1 gene (which encodes the MED25 subunit of the Mediator complex) is required for the uncompromised expression of both salicylic acid- and jasmonate-dependent defense genes as well as resistance to the leaf-infecting fungal pathogens, Alternaria brassicicola and Botrytis cinerea in Arabidopsis. Surprisingly, we found that the pft1/med25 mutant showed increased resistance to the root infecting pathogen Fusarium oxysporum and that this resistance was independent of classical defense genes. In addition, the over-expression of PFT1 led to increased susceptibility to F. oxysporum. Therefore, to explore this phenomenon further, we wished to use whole genome transcript profiling to identify which genes may be playing a role in pft1/med25-mediated resistance to F. oxysporum. Experiment Overall Design: We grew both WT and pft1/med25 plants for four weeks in soil. After four weeks we treated the plants by root-dipping in either water or a F. oxysporum spore suspension before replanting them back into soil. There were four independent replicates of each treatment and each replicate contained 20 plants each. The treatments were WT (mock): pft1 (mock): WT (infected): pft1 (infected). Each replicate (16 in total) was harvested after 48 hours and the resulting RNA was used for hybridization to an Affymetrix ATH1 chip.

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Maize gene expression during infection with Fusarium moniliforme

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