Microarray analysis of elp2 and wild type (Col-0) infected with the necrotrophic fungal pathogen Botrytis cinerea
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE48207 | GEO | 2013/07/01
SECONDARY ACCESSION(S): PRJNA209201
REPOSITORIES: GEO
Similar Datasets
Project description:The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutant elp2 and wild type in response to infection of the necrotrophic fungal pathogen Botrytis cinerea. Results indicated that, compared with the wild type, the WRKY33/OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59 (ORA59)/ETHYLENE RESPONSE FACTOR1 transcriptional cascades are down-regulated, whereas the MYC2 transcriptional cascade is up-regulated in the elp2 mutant. Three biological replicates with leaves from 8-12 plants per sample were collected at 0, 3, 6, 12, 24, and 48 hours after inoculation with the necrotrophic fungal pathogen Botrytis cinerea. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Equal amount of RNA from the 3 biological replicates were used for microarray analysis. The channels of the dual-channel arrays were analyzed independently.
2013-07-01 | E-GEOD-48207 | biostudies-arrayexpress
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.
2015-06-15 | GSE66290 | GEO
Project description:The Arabidopsis thaliana mutant wrky33 is highly susceptible to the necrotrophic fungus Botrytis cinerea. We identified by ChIP-seq >1680 high-confidence WRKY33 binding sites associated with 1576 genes within the Arabidopsis genome, with all of them being dependent on rapid activation of WRKY33 expression by Botrytis cinerea strain 2100. Genome-wide transcriptional analysis defined 318 genes as direct functional targets at 14 h post inoculation. Comparison between resistant wild-type Columbia-0 and susceptible wrky33 mutant plants revealed that expression of 75% of all WRKY33 regulated targets were down-regulated upon infection, indicating that WRKY33 predominately acts as a repressor. However, WRKY33 appears to possess dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. Our genome-wide analysis confirmed known WRKY33 targets involved in ethylene and jasmonic acid hormone signaling and phytoalexin biosynthesis, but also uncovered a previously unknown role of abscisic acid (ABA) biosynthesis in the complex regulatory circuitry affecting resistance towards Botrytis.
2015-06-15 | GSE66289 | GEO
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
Project description:The Arabidopsis thaliana mutant wrky33 is highly susceptible to the necrotrophic fungus Botrytis cinerea. We identified by ChIP-seq >1680 high-confidence WRKY33 binding sites associated with 1576 genes within the Arabidopsis genome, with all of them being dependent on rapid activation of WRKY33 expression by Botrytis cinerea strain 2100. Genome-wide transcriptional analysis defined 318 genes as direct functional targets at 14 h post inoculation. Comparison between resistant wild-type Columbia-0 and susceptible wrky33 mutant plants revealed that expression of 75% of all WRKY33 regulated targets were down-regulated upon infection, indicating that WRKY33 predominately acts as a repressor. However, WRKY33 appears to possess dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. Our genome-wide analysis confirmed known WRKY33 targets involved in ethylene and jasmonic acid hormone signaling and phytoalexin biosynthesis, but also uncovered a previously unknown role of abscisic acid (ABA) biosynthesis in the complex regulatory circuitry affecting resistance towards Botrytis. Analysis of transgenic plants expressing WRKY33-HA under its native promoter post inoculation with spores of Botrytis cinerea 2100
2015-06-15 | E-GEOD-66289 | biostudies-arrayexpress
Project description:The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutants med16, med8, elp2, wild type in response to infection of the necrotrophic fungal pathogen Sclerotinia sclerotiorum. Results indicated that, compared with the wild type, the jasmonic acid (JA) biosynthesis genes LOX3, AOC3, and OPR3, ethylene (ET) biosynthesis genes ACS2 and ACS8, as well as salicylic acid (SA) biosynthesis genes ICS1 and EDS5 were up-regulated in med16 in local tissues at 1 day post-inoculation (dpi) and/or systemic tissues at 4 dpi. Surprisingly, however, while a number of SA pathway genes (EDS1, PAD4, NPR1, WRKY18, WRKY38, WRKY53, PR1, and PR2) and several JA-regulated wound-responsive genes (MYC2, JAR1, VSP1, and VSP2) were up-regulated in med16, a group of JA/ET-regulated defense genes (ORA59, ERF1, ERF14, PDF1.2, PDF1.2b, PDF1.2c, PDF1.3, PR4, and ChiB) and PR5 were down-regulated. On the other hand, only a few of these genes were differentially expressed between med8 or elp2 and the wild type.
2015-01-22 | GSE65165 | GEO
Project description:The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutants med16, med8, elp2, wild type in response to infection of the necrotrophic fungal pathogen Sclerotinia sclerotiorum. Results indicated that, compared with the wild type, the jasmonic acid (JA) biosynthesis genes LOX3, AOC3, and OPR3, ethylene (ET) biosynthesis genes ACS2 and ACS8, as well as salicylic acid (SA) biosynthesis genes ICS1 and EDS5 were up-regulated in med16 in local tissues at 1 day post-inoculation (dpi) and/or systemic tissues at 4 dpi. Surprisingly, however, while a number of SA pathway genes (EDS1, PAD4, NPR1, WRKY18, WRKY38, WRKY53, PR1, and PR2) and several JA-regulated wound-responsive genes (MYC2, JAR1, VSP1, and VSP2) were up-regulated in med16, a group of JA/ET-regulated defense genes (ORA59, ERF1, ERF14, PDF1.2, PDF1.2b, PDF1.2c, PDF1.3, PR4, and ChiB) and PR5 were down-regulated. On the other hand, only a few of these genes were differentially expressed between med8 or elp2 and the wild type. Three biological replicates with leaves from 8-12 plants per sample were collected at 0, 1, 2, and 4 days post-inoculation (dpi) after inoculation with the necrotrophic fungal pathogen Sclerotinia sclerotiorum. Leaf tissues were collected as controls at 0 dpi, the inoculated leaves were collected as local tissues at 1 dpi, and the upper uninoculated leaves were collected as systemic tissues at 2 and 4 dpi. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Equal amount of RNA from the 3 biological replicates were used for microarray analysis.
2015-01-22 | E-GEOD-65165 | biostudies-arrayexpress
Project description:To define how DRL1 regulates Botrytis cinerea-induced transcriptional changes at the genome level, we performed a microarray experiment on B. cinerea-infected drl1 and wild-type plants to identify genes that were differentially expressed between drl1 and the wild type. A total of 200 defense response genes were differentially expressed between drl1 and the wild type at six hours post-inoculation. These genes include 20 ethylene (ET) responsive genes, 23 jasmonic acid (JA)/ET responsive genes, 50 JA responsive genes, and 107 other defense genes. All ET and JA/ET responsive genes and majorities of JA responsive and other defense genes were down-regulated in the drl1 mutant. Among the down-regulated genes are a group of well-characterized defense genes, including ORA59, ERF1, WRKY33, SIB1, PAD3, GLIP1, and CYP79B2, which have been demonstrated to function in resistance to necrotrophic fungal pathogens, indicating that DLR1 may contribute to B. cinerea resistance by modulating the expression of these defense genes.
2019-09-23 | GSE79961 | GEO
Project description:Worldwide, 20-25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply handling chain due to spoilage by fungal pathogens. Most impactful postharvest pathogens exhibit necrotrophic lifestyles, resulting in rotting of the host tissues and complete loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. However, these pathogens generally fail to infect unripe fruit, or remain quiescent until host and environmental conditions stimulate a successful infection. Current research on necrotrophic infections of fruit was mainly focused on the host by characterizing genetic and physicochemical factors that inhibit or promote the disease. However, the pathogenicity and virulence strategies employed by necrotrophic pathogens in ripe and unripe fruit are mostly understudied. Here, we provide a first comparative transcriptomics study of fungal postharvest pathogens: Botrytis cinerea, Rhizopus stolonifer and Fusarium acuminatum, all of which display necrotrophic behavior when infecting fruit. We de novo assembled and annotated the transcriptomes of R. stolonifer, and F. acuminatum and performed a differential gene expression analysis comparing the three fungal transcriptomes during fruit infection with that of fungal in-vitro growth. Analysis of the differentially expressed genes for enrichment of functional annotations revealed shared strategies of the three fungi during infection of compatible (ripe fruit) and incompatible (unripe fruit) hosts. We furthermore selected candidate genes that are involved in these strategies to characterize their expression during infection of unripe and ripe-like fruit of the non-ripening (nor) tomato mutant, both of which are physiologically and biochemically similar to unripe wildtype fruit. By enabling a better understanding of fungal necrotrophic infection strategies, we move closer to generating accurate models of fruit diseases and development of early detection tools and effective management strategies.
2018-12-01 | GSE122555 | GEO
Project description:Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
| S-EPMC3158057 | biostudies-literature