Phytophthora infestans PIC99189
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ABSTRACT:
PROVIDER: PRJEA52687 | ENA |
REPOSITORIES: ENA
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Project description:Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level. Phytophthora infestans mycelium small RNAs were sequenced and aligned to the P. infestans genome for analysis.
2013-10-21 | E-GEOD-50030 | 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:Phytophthora infestans Genome sequencing
| PRJNA185334 | ENA
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
Project description:Phytophthora infestans Genome sequencing and assembly
| PRJNA592863 | ENA
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.
2023-10-19 | GSE215998 | GEO
Project description:Phytophthora infestans 90128 genome sequencing
| PRJEA52693 | ENA
Project description:Phytophthora infestans genome sequencing project
| PRJNA52435 | ENA