Phytophthora infestans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA12766 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR160348_1.fastq.gz | Fastqsanger.gz | |||
| DRR160348_2.fastq.gz | Fastqsanger.gz | |||
| DRR160349_1.fastq.gz | Fastqsanger.gz | |||
| DRR160349_2.fastq.gz | Fastqsanger.gz |
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Project description:A screen for genes induced during sexual development was performed in the heterothallic oomycete Phytophthora infestans, the potato blight agent. Of 15,644 unigenes on the Affymetrix chip, 87 were induced >10-fold during mating, with 28 induced >100-fold. This was subsequently validated in independent matings using RNA blots and RT-PCR. Keywords: Developmental stage comparison
2007-03-30 | GSE6343 | GEO
Project description:Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that leads to Irish potato famine and threatens world-wide food security. Despite the genome of P. infestans has provided fundamental resource for studying the aggressiveness of this pandemic pathogen, the epigenomes remain poorly understood. Here, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we demonstrate post-translational modifications (PTM) at P. infestans core histone H3. The PTMs not only include these prevalent modifications in eukaryotes, and also some novel marks, such as H3K53me2 and H3K122me3. We focused on the trimethylations of H3K4, H3K9 and H3K27 and H3K36, and profiled P. infestans epigenomes employing Native Chromatin Immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromomatin accessibility by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3, and are generally in condense chromatin. Interestingly, we observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions that barely have the four histone modifications. With a combination of genomic, epigenomic, transcriptomic strategies, our study illustrates the epigenetic states in P. infestans, which will help to study genomic functions and regulations in this pathogen.
2024-03-24 | GSE199295 | GEO
Project description:Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that leads to Irish potato famine and threatens world-wide food security. Despite the genome of P. infestans has provided fundamental resource for studying the aggressiveness of this pandemic pathogen, the epigenomes remain poorly understood. Here, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we demonstrate post-translational modifications (PTM) at P. infestans core histone H3. The PTMs not only include these prevalent modifications in eukaryotes, and also some novel marks, such as H3K53me2 and H3K122me3. We focused on the trimethylations of H3K4, H3K9 and H3K27 and H3K36, and profiled P. infestans epigenomes employing Native Chromatin Immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromomatin accessibility by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3, and are generally in condense chromatin. Interestingly, we observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions that barely have the four histone modifications. With a combination of genomic, epigenomic, transcriptomic strategies, our study illustrates the epigenetic states in P. infestans, which will help to study genomic functions and regulations in this pathogen.
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Project description:The oomycete Phytophthora infestans is the causal agent of late blight in potato and tomato. Since the underlying processes that govern pathogenicity and development in P. infestans are largely unknown, we have performed a large-scale phosphoproteomics study of six different P. infestans life stages. We have obtained quantitative data for 2922 phosphopeptides and compared their abundance in different life stages. The samples were analysed on an LTQ Orbitrap XL ETD, operated in data dependent mode to automatically perform Orbitrap-MS and LTQ-MS/MS analysis. The raw data from the Orbitrap was converted to .mgf files using ProteoWizard. The Proteios software environment was used to search the mgf files with Mascot version 2.3.01 against a database consisting of all P. infestans proteins in UniProt as of 2010-04-22, concatenated with an equal size decoy database (random protein sequences with conserved protein length and amino acid distribution, in total 36,512 target and decoy protein entries). Search tolerances were set to 7 ppm for MS and 0.5 Da for MS/MS. One missed cleavage was allowed. Carbamidomethylation of cysteine residues was selected as a fixed modification and oxidation of methionine residues and phosphorylation of serine, threonine and tyrosine residues were selected as variable modifications. Search results were exported from Mascot as XML, including query level results, with a modification to the export script to include protein accession numbers also for the query (spectrum) level results. All search results, including the top ranked peptide for each spectrum, were imported to Proteios, where q values were calculated using the target-decoy method.
2014-03-27 | PXD000433 | Pride
Project description:Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that leads to Irish potato famine and threatens world-wide food security. Despite the genome of P. infestans has provided fundamental resource for studying the aggressiveness of this pandemic pathogen, the epigenomes remain poorly understood. Here, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we demonstrate post-translational modifications (PTM) at P. infestans core histone H3. The PTMs not only include these prevalent modifications in eukaryotes, and also some novel marks, such as H3K53me2 and H3K122me3. We focused on the trimethylations of H3K4, H3K9 and H3K27 and H3K36, and profiled P. infestans epigenomes employing Native Chromatin Immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromomatin accessibility by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3, and are generally in condense chromatin. Interestingly, we observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions that barely have the four histone modifications. With a combination of genomic, epigenomic, transcriptomic strategies, our study illustrates the epigenetic states in P. infestans, which will help to study genomic functions and regulations in this pathogen.
2024-03-24 | GSE199297 | GEO
Project description:Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that was responsible for the Irish potato famine and continues to threaten global food security. While the P. infestans genome is an excellent resource for studying the aggressiveness of this pandemic pathogen, its epigenome remains poorly understood. In this study, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified post-translational modifications (PTMs) at the P. infestans core histone H3. The PTMs include prevalent modifications in eukaryotes, as well as some novel marks, such as H3K53me2 and H3K122me3. We focused on trimethylations of H3K4, H3K9, H3K27, and H3K36, and profiled the P. infestans epigenome using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromatin accessibility using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3 and are generally found in condensed chromatin. Interestingly, highly accessible regions with ATAC-seq peaks are also found in this compartment. We observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions with few histone modifications. Based on N-ChIP-seq at 3 days post-incubation, we revealed the PTM dynamics in secretome genes from the mycelium to the infection stage. Using a combination of genomic, epigenomic, and transcriptomic strategies, our study illustrates the epigenetic states and changes in P. infestans, helping to elucidate genomic functions and regulation in this pathogen.
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Project description:Much of the pathogenic success of Phytophthora infestans, the potato and tomato late blight agent, relies on its ability to generate from mycelia large amounts of sporangia, which release zoospores that encyst and form infection structures. To better understand these critical stages, Affymetrix GeneChips based on 15,650 unigenes were designed and used to profile the life cycle, through an analysis of RNA from hyphae, sporangia, cleaving sporangia, motile zoospores, and germinated zoospore cysts. Keywords: Developmental study
2008-03-15 | GSE9623 | GEO
Project description:RNA-sequencing data of three potato cultivars (Deisree, Sarpo Mira and SW92-1015) with different susceptibility to Phytopthora infestans causing late blight 24 hours post P. infestans infection
2014-06-26 | E-MTAB-1712 | 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:Late blight caused by Phytophthora infestans seriously threatens world’s potato production. Understanding the responsive mechanism of potato to P. infestans infection and exploring key regulators would be advantageous for improving the late blight resistance. Here, we assess the late blight resistance of various potato cultivars from Liangshan Yi Autonomous Prefecture and identified Chuan Liang Shu 10 (CLS) with strong resistant, while Bu Wu Yu (BWY) is highly susceptible. Comparative transcriptomics between these two cultivars upon P. infestans inoculation reveal that CLS activates defense pathways rapidly, while BWY prioritizes energy towards growth and development pathways, resulting in distinct late blight resistances. Specifically, the resistance of CLS might be contributed by enhanced oxidation-reduction process and SA signaling. Clustering analysis of the expression patterns for transcription factors (TFs) demonstrates that the WRKY family members play important roles in late blight resistance of CLS, among which StWRKY26 is identified as a positive regulator of late blight resistance. Silencing of StWRKY26 in CLS significantly compromise its intrinsic resistance to P. infestans. Our study enriches the knowledge of transcriptional responses of potato under P. infestans infection and provide candidate genes for breeding potato cultivars with strong late blight resistance.
2025-06-30 | GSE270562 | GEO