Phytophthora infestans
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PROVIDER: PRJNA111491 | ENA |
REPOSITORIES: ENA
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Project description:Expression analysis of Phytophthora infestans isolates 06_3928A and NL07434 during potato infection 2-4 days post-inoculation
| PRJNA149417 | ENA
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:The expression of genes in P. infestans was monitored over a five day time course of a potato infection. Genes encoding known and putative effector proteins were found induced at two days post-inoculation with expression decaying over the five day time course.
2009-02-16 | GSE14480 | 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.
2012-09-01 | GSE33240 | GEO
Project description:The late blight pathogen, Phytophthora infestans has a broad host range within the Solanaceae family, including yellow potato (Solanum phureja). The disease caused by P. infestans in S. phureja is poorly understood and is a major concern in Colombia. Expressed Sequence Tag (EST) libraries obtained from a normalized library constructed from healthy plant tissue revealed high levels of sequence similarity between S. phureja and S. tuberosum. Then, utilizing Serial Analysis of Gene Expression and high-throughput sequencing (SAGE-Solexa), we characterized yellow potato gene expression during infection by P. infestans. Four-week-old yellow potato plants were inoculated with P. infestans and were collected at 12 and 72 hours post inoculation for RNA extraction. We detected differentially expressed genes by comparing inoculated to non-inoculated and resistant to susceptible plants. The discovery and characterization of the proteins mediating this host–pathogen interaction enable the understanding of the pathosystem and is the key for developing resistant plants. Keywords: SAGE-Solexa, inoculation response, transcript profiling, Solanum phureja, Phytophthora infestans
2009-06-13 | GSE11781 | GEO
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 Second full expanded leaves from both healthy tomato plants (non-inoculated) and diseased tomato plants inoculated with Phytophthora infestans inoculum were used to extract total RNA for microarry analysis 12 hours post inoculation time.
2011-10-24 | E-GEOD-33177 | biostudies-arrayexpress
Project description:The late blight pathogen, Phytophthora infestans has a broad host range within the Solanaceae family, including yellow potato (Solanum phureja). The disease caused by P. infestans in S. phureja is poorly understood and is a major concern in Colombia. Expressed Sequence Tag (EST) libraries obtained from a normalized library constructed from healthy plant tissue revealed high levels of sequence similarity between S. phureja and S. tuberosum. Then, utilizing Serial Analysis of Gene Expression and high-throughput sequencing (SAGE-Solexa), we characterized yellow potato gene expression during infection by P. infestans. Four-week-old yellow potato plants were inoculated with P. infestans and were collected at 12 and 72 hours post inoculation for RNA extraction. We detected differentially expressed genes by comparing inoculated to non-inoculated and resistant to susceptible plants. The discovery and characterization of the proteins mediating this host–pathogen interaction enable the understanding of the pathosystem and is the key for developing resistant plants. Keywords: SAGE-Solexa, inoculation response, transcript profiling, Solanum phureja, Phytophthora infestans Four-week-old yellow potato (Solanum phureja) plants were inoculated with Phytophthora infestans and were collected and flash frozen in liquid nitrogen at 12 and 72 hours post inoculation, as well as mock inoculated, for RNA extraction. 2 yellow potato cultivars (resistant and susceptible) were used for each experiment. Mock inoculated plants were collected in each replicate. RNA obtained from each of the three biological replicates was pooled to obtain a single RNA sample for each timepoint X cultivar combination. A total of 6 different SAGE libraries were thus obtained. For all libraries, Illumina sequencing was performed at Canada´s Michael Smith Genome Sciences Centre.
2009-06-13 | E-GEOD-11781 | 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, 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:Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results: To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions: Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans. Small RNA sequence data from Phytophthora infestans-infected potato leaf tissue and P. infestans mycelium tissue. Three infection stage time-points. Two P. infestans lines: 88089 (wild-type) and PiDcl1 (transformant PiDcl1 knock-down). No replicates. Total number of samples: 8.
2014-12-12 | E-GEOD-63292 | biostudies-arrayexpress