Germination and appressorium formation in Magnaporthe grisea
Ontology highlight
ABSTRACT:
ORGANISM(S): Magnaporthe grisea
SUBMITTER: Sean Coughlan
PROVIDER: E-GEOD-1945 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE8517: Magnaporthe oryzae gene expression during biotrophic invasion of rice using version 2 of the Agilent Magnaporthe grisea Array (G4137B). GSE8518: Rice gene expression during biotrophic invasion by the rice blast fungus Magnaporthe oryzae using the Agilent Rice Array (G4138A). Keywords: SuperSeries Refer to individual Series
2009-04-08 | E-GEOD-8670 | biostudies-arrayexpress
Project description:The hemibiotrophic fungus Magnaporthe oryzae produces specialized biotrophic invasive hyphae (IH) that alter membrane structure and defense responses in invaded rice cells. IH successively invade live neighbor cells, apparently through plasmodesmata. Understanding fungal and rice genes that contribute to biotrophic invasion has been a challenge because so few plant cells have encountered IH at the earliest infection stages. Using a rice sheath inoculation method, we successfully enriched for infected tissue RNA that contained ~20% fungal RNA at a point when most IH were still growing in first-invaded rice cells. The RNAs were analyzed using the whole-genome M. oryzae oligoarray and a rice oligoarray. Rice genes that were induced >50-fold during infection were enriched for genes involved in transferring information from sensors to cellular responses. Fungal genes that were induced >50-fold in IH included the PWL2 avirulence gene and genes encoding hypothetical secreted proteins. The IH-specific secreted proteins are candidate effectors, proteins that the fungus secretes into live host cells to control cellular processes. Gene knock-out analyses of three putative effector genes failed to show major effects on pathogenicity. Details of the blast interaction transcriptome will provide insights on the mechanisms of biotrophic plant disease. Keywords: Disease state analysis Our goal was to compare expression in biotrophic IH to expression in mycelium grown in nutrient medium, and to compare expression in infected rice sheath to expression in mock inoculated rice. Using version 2 of the fungal whole genome microarray (Agilent Technologies), we analyzed samples from three biological replicates of rice leaf sheath at 36 hours after inoculation with the rice blast fungus M. oryzae. The same samples were used with the Agilent rice microarray (see series GSE8518). To estimate the ratio of fungal to rice RNAs in the infected sheaths, we compared RT-PCR amplification of fungal genes in infected tissue to amplification in standards produced by mixing known ratios of pure mycelial RNA with mock-inoculated rice RNA. Using this assay, fungal RNA content in infected tissues were approximately 20% of the total RNAs. We prepared control mixtures by pooling 20% mycelial RNA and 80% RNA from mock-inoculated rice sheath. Complementary RNAs from infected tissues were labeled with Cy3 or Cy5 and hybridized together with the control mixture RNA labeled with the other dye. Three independent biological replications were performed, with separate hybridizations for 2 technical replications and corresponding dye swap experiments. Data were analyzed by Rosetta Resolver® and showed a correlation of over 80% between biological replications.
2009-04-08 | E-GEOD-8517 | biostudies-arrayexpress
Project description:The hemibiotrophic fungus Magnaporthe oryzae produces specialized biotrophic invasive hyphae (IH) that alter membrane structure and defense responses in invaded rice cells. IH successively invade live neighbor cells, apparently through plasmodesmata. Understanding fungal and rice genes that contribute to biotrophic invasion has been a challenge because so few plant cells have encountered IH at the earliest infection stages. Using a rice sheath inoculation method, we successfully enriched for infected tissue RNA that contained ~20% fungal RNA at a point when most IH were still growing in first-invaded rice cells. The RNAs were analyzed using the whole-genome M. oryzae oligoarray and a rice oligoarray. Rice genes that were induced >50-fold during infection were enriched for genes involved in transferring information from sensors to cellular responses. Fungal genes that were induced >50-fold in IH included the PWL2 avirulence gene and genes encoding hypothetical secreted proteins. The IH-specific secreted proteins are candidate effectors, proteins that the fungus secretes into live host cells to control cellular processes. Gene knock-out analyses of three putative effector genes failed to show major effects on pathogenicity. Details of the blast interaction transcriptome will provide insights on the mechanisms of biotrophic plant disease. Experiment Overall Design: Our goal was to compare expression in infected rice sheath to expression in mock inoculated rice, and to compare expression in biotrophic IH to expression in mycelium grown in nutrient medium. Using the rice microarray (Agilent Technologies), we analyzed samples from three biological replicates of rice leaf sheath at 36 hours after inoculation with the rice blast fungus M. oryzae. The same samples were used with the Agilent M. oryzae microarray (see series GSE8517). To estimate the ratio of fungal to rice RNAs in the infected sheaths, we compared RT-PCR amplification of fungal genes in infected tissue to amplification in standards produced by mixing known ratios of pure mycelial RNA with mock-inoculated rice RNA. Using this assay, fungal RNA content in infected tissues were approximately 20% of the total RNAs. We prepared control mixtures by pooling 20% mycelial RNA and 80% RNA from mock-inoculated rice sheath. Complementary RNAs from infected tissues were labeled with Cy3 or Cy5 and hybridized together with the control mixture RNA labeled with the other dye. Three independent biological replications were performed, with separate hybridizations for 2 technical replications and corresponding dye swap experiments. Data were analyzed by Rosetta Resolver® and showed a correlation of over 80% between biological replications.
2009-04-17 | E-GEOD-8518 | biostudies-arrayexpress
Project description:This experiment was designed to analyze transcriptional changes that occur when the fungal plant pathogen M. grisea is shifted from a complete media to a nitrogen-starved media. Comparisons were made in the following way between fungal mycelial grown in minimal media supplemented with a nitrogen source (MM+N) and minimal media without a nitrogen source (NS) Keywords: parallel sample
2010-07-01 | E-GEOD-2716 | biostudies-arrayexpress
Project description:This series examines differential gene expression during germination and appressorium formation by the rice blast fungus Magnaporthe grisea. Conidia were germinated on either the hydrophobic (inductive) or hydrophilic (non-inductive) side of GelBond. RNA was extracted from conidia and following incubation for 7 and 12 hours. RNA from two biological replications of each treatment was pooled in equal amounts and labeled with both cy3 and cy5 dyes using the Agilent Technologies Low Input Linear Amplification Kit. Hybridizations were performed on Agilent Technologies whole genome oligo rice blast arrays (product G4137A) using manufacturer prescribed protocols and reagents in an interlaced loop design in which each treatment was paired with every other. This series contains a total of 10 hybridizations; each treatment was used in 4 hybridizations (2 with cy3 and 2 cy5). Spot fluorescence was normalized using Lowess within and between microarray slides in Bioconductor and gene expression profiles analyzed in GeneSpring. Keywords: other
2004-11-10 | GSE1945 | GEO
Project description:This series examines differential gene expression during appressorium formation induced by exogeous cyclic AMP in the rice blast fungus Magnaporthe grisea. RNA was extracted from spores germinated on hydrophilic (non-inductive) side of GelBond as well as from spores elaborating appressia on hydrophilic surfaces in the presence of cAMP after 9 hrs incubation. RNA from two biological replications of each treatment was pooled in equal amounts and labeled with both cy3 and cy5 dyes using the Agilent Technologies Low Input Linear Amplification Kit. Hybridizations were performed on Agilent Technologies whole genome oligo rice blast arrays (product G4137B) using manufacturer prescribed protocols and reagents in an reference design in which each treatment was paired with every other. This series contains a total of 4 hybridizations; each treatment was used in 4 hybridizations (2 with Cy3 and 2 Cy5). Spot fluorescence was normalized using Lowess within and between microarray slides in Bioconductor. Keywords: Cell development
2008-01-15 | GSE10173 | GEO
Project description:This series examines differential gene expression during appressorium formation induced by exogeous cyclic AMP in the rice blast fungus Magnaporthe grisea. RNA was extracted from spores germinated on hydrophilic (non-inductive) side of GelBond as well as from spores elaborating appressia on hydrophilic surfaces in the presence of cAMP after 9 hrs incubation. RNA from two biological replications of each treatment was pooled in equal amounts and labeled with both cy3 and cy5 dyes using the Agilent Technologies Low Input Linear Amplification Kit. Hybridizations were performed on Agilent Technologies whole genome oligo rice blast arrays (product G4137B) using manufacturer prescribed protocols and reagents in an reference design in which each treatment was paired with every other. This series contains a total of 4 hybridizations; each treatment was used in 4 hybridizations (2 with Cy3 and 2 Cy5). Spot fluorescence was normalized using Lowess within and between microarray slides in Bioconductor. Keywords: Cell development Two-condition experiment, cyclic AMP treated vs. non treated spores. 4 biological replicates with dye-swaps
2010-05-26 | E-GEOD-10173 | biostudies-arrayexpress
Project description:Microarray analysis was used to compare different developmental stages of the filamentous fungus Aspergillus nidulans. Cells were grown for various times and comparisons made between: 1. Isolated conidia (0 hours) and isotropically expanding cells (3 hours). 2. Isotropically expanding cells (3 hours) and polarly extending cells (5 hours). 3. Undifferentiated vegetative hyphae (18 hours) and synchronously conidiating cultures (42 hours). A total of 4 hybridizations were performed for each microarray experiment described in the summary. The following replicates were carried out: 1. Two biological replicates were performed using cultures grown in parallel. 2. Two Technical ‘dye swap’ replicates were carried out for each biological replicate.
2008-05-01 | E-GEOD-7698 | biostudies-arrayexpress
Project description:Conidia from null mutants strains for the genes CDC42, RHO4, BUF1, SLN1 as well as the wild-type Guy11 were harvested and placed on an inductive surface. After 16 hours developing appressoria were harvested and transcript abundance analysed using RNA-seq, two biological replicates per sample.
2019-07-18 | GSE118095 | GEO
Project description:Histoplasma capsulatum is a fungal pathogen that infects both healthy and immunocompromised hosts. In endemic regions, H. capsulatum grows in the soil and causes respiratory and systemic disease when inhaled by humans. An interesting aspect of H. capsulatum biology is that it adopts specialized developmental programs in response to its environment. In the soil, it grows as filamentous chains of cells (mycelia) that produce asexual spores (conidia). When the soil is disrupted, conidia aerosolize and are inhaled by mammalian hosts. Inside a host, conidia germinate into yeast-form cells that colonize immune cells and cause disease. Despite the ability of conidia to initiate infection and disease, they have not been explored on a molecular level. Here we develop methods to purify H. capsulatum conidia and show that these cells germinate into either filaments at room temperature or into yeast-form cells at 37C. Conidia internalized by macrophages germinate into the yeast form and proliferate within the macrophages, ultimately lysing the host cells. Similarly, infection of mice with purified conidia is sufficient to establish infection and yield viable yeast-form cells in vivo. To characterize conidia on a molecular level, we perform whole-genome expression profiling of conidia, yeast, and mycelia from two highly diverged H. capsulatum strains. In parallel, we use homology and protein domain analysis to manually annotate the predicted genes of both strains. Analyses of the resultant data define sets of transcripts that reflect the unique molecular states of H. capsulatum conidia, yeast and mycelia. This series gives the results for the G217B strain. Samples were labeled with Cy5 or with Cy3 and competitively hybridized to custom glass slide 70-mer oligomer microarrays in a closed-circuit experimental design (e.g. direct, pairwise comparisons of yeast and mycelial samples, mycelial and conidial samples, and yeast and conidial samples). Dye-swap hybridizations were performed for these pairwise comparisons, and hybridizations to an additional conidial biological replicate were performed for the conidia/yeast and conidia/mycelia comparisons, for a total of 8 hybridizations.
2013-04-10 | E-GEOD-45415 | biostudies-arrayexpress