Phytophthora infestans gene expression during potato infection 2-5 days post inoculation
Ontology highlight
ABSTRACT:
ORGANISM(S): Phytophthora infestans Solanum lycopersicum
PROVIDER: GSE14480 | GEO | 2009/02/16
SECONDARY ACCESSION(S): PRJNA111491
REPOSITORIES: GEO
Similar Datasets
Project description:The expression of genes in P. infestans isolates 06_3928A and NL07434 was monitored from 2 to 4 days time course of a potato infection. Genes encoding known and putative effector proteins were found induced at two and/or three days post-inoculation.
2012-09-01 | GSE33240 | GEO
Project description:Time course study of potato leaves from three cultivars (cv. Desiree, Sarpo Mira, SW-1015) 6, 24 and 72 hours after P. infestans infection
2014-06-23 | E-MTAB-1515 | biostudies-arrayexpress
Project description:Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Reports suggest that pathogen-derived sRNAs can modulate the expression of plant defense genes. The experiments reported here were designed to shed light on impact of sRNAs in the potato-P. infestans interaction. We used the Argonaute or Ago1 from P. infestans tagged with GFP transformed into the 88069 strain to infect potato cv. Bintje plants. Collected leaf materials were used in co-immunoprecipitation experiments together with P. infestans harboring GFP (control GFP) and P. infestans mycelia grown on media (control mycelia). These three materials were sequenced at a Ion Proton platform. The reads length of 8-38 nt were adaptor-trimmed and mapped to the P. infestans genome and the Solanom tuberosum genome v4.04. Both P. infestans-associated and potato derived sRNAs were identified.
2021-06-30 | GSE119230 | GEO
Project description:The expression of genes in P. infestans isolates 06_3928A and NL07434 was monitored from 2 to 4 days time course of a potato infection. Genes encoding known and putative effector proteins were found induced at two and/or three days post-inoculation. We used a custom chip GPL8093 from Roche Nimblegen’s proprietary Maskless Array Synthesis (MAS) technology uses digital light processing and rapid, high-yield photochemistry to synthesize long oligo, high-density DNA microarrays with extreme flexibility. Each GPL8093 chip measures the expression level of 18155 genes from Phytophthora infestans with 60-mer probe pairs (PM/MM) per gene. Total RNA samples recovered from mycelia in two medias (rye sucrose agar and V8 agar) and infected potato leaves from a time couse infection (2, 3 and 4 days post incoulation). Experiments included two biological repllicates from each sample. We carried out total RNA extractions (mycelia and potato infected material) for two P. infestans isolates 06_3928A and NL07434. cDNA synthesis was performed Nimblegen.
2012-09-01 | E-GEOD-33240 | biostudies-arrayexpress
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:Potato Late blight is one the most important crop diseases worldwide. Even though potato has been studied for many years, the potato disease late blight still has a huge negative effect on the potato production. A total of three commercially available field potato cultivars of different resistance to late blight infection: Kuras (moderate), Sarpo Mira (highly resistant) and Bintje (very suseptable) under controlled green house growing conditions innoculated with a diversity of P. infestans populations. We used label-free quantitative proteomics to investigate the infection with P. infestans in a time-course study over 258 hours. Several key issues limits proteome analysis of potato leaf tissue4–6. Firstly, the immense complexity of the plant proteome which is further complicated by the presence of highly abundant proteins, such as ribulose bisphosphate carboxylase/oxygenase (RuBisCO). Secondly, plant leaf and potato in particular contain abundant levels amounts of phenols and polyphenols which hinder or, unless precautions are taken, completely prevent a successful protein extraction.
2016-01-05 | PXD002767 | Pride
Project description:<p>Late blight is one of the main biological stresses limiting the potato yield; however, the biochemical mechanisms underlying the infection process of <em>Phytophthora infestans</em> remain unrevealed. In this study, the late blight-resistant potato cultivar Ziyun No.1 (R) and the susceptible cultivar Favorita (S) were inoculated with <em>P. infestans</em>. Untargeted metabolomics was used to study the changes of metabolites in the compatible and incompatible interactions of the two cultivars and the pathogen at 0, 48 and 96 h postinoculation (hpi). A total of 819 metabolites were identified, and the metabolic differences mainly emerged after 48 hpi. There were 198 and 115 differentially expressed metabolites (DEMs) in the compatible and incompatible interactions. These included 147 and 100 upregulated metabolites during the compatible and incompatible interactions, respectively. Among them, 73 metabolites were identified as the <em>P. infestans</em>-responsive DEMs. Furthermore, the comparisons between the two cultivars identified 57 resistance-related metabolites. Resistant potato cultivar had higher levels of salicylic acid and several upstream phenylpropanoid biosynthesis metabolites, triterpenoids and hydroxycinnamic acids and their derivatives, such as sakuranetin, ferulic acid, ganoderic acid Mi, lucidenic acid D2 and caffeoylmalic acid. These metabolites play crucial roles in cell wall thickening and have antibacterial and antifungal activities. This study reports the time-course metabolomic responses of potatoes to <em>P. infestans</em>. The findings reveal the responses involved in the compatible and incompatible interactions of potatoes and <em>P. infestans</em>.</p>
2022-05-20 | MTBLS4365 | MetaboLights
Project description:Oomycetes are filamentous organisms that cause notorious diseases, several of which with high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focussed on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyse P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment.
2016-07-09 | PXD000802 | 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 | GSE199296 | 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