Profiling the asexual development transcriptome of the late blight pathogen Phytophthora infestans
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ABSTRACT:
ORGANISM(S): Phytophthora infestans
PROVIDER: GSE9623 | GEO | 2008/03/15
SECONDARY ACCESSION(S): PRJNA103475
REPOSITORIES: GEO
Similar Datasets
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 Gene expression in non-sporulating hyphae, asexual sporangia, sporangia undergoing cleavage, swimming zoospores, and germinated cysts containing appressoria were characterized using isolate 88069. Several strategies controlled for experimental error. Firstly, two replicate hybridizations were used for each tissue type. Secondly, RNAs for the two replicates were prepared by research groups in North America and/or Europe. Thirdly, RNA for each hybridization was pooled from two or three independent cultures made by that group. Finally, before using an RNA sample in an experiment the expression of selected well-characterized genes was measured to ensure that the tissue was properly prepared.
2008-03-14 | E-GEOD-9623 | biostudies-arrayexpress
Project description:Samples were isolated from six different P. infestans life stages (hyphae, sporangia, zoospores, cysts, germinated cysts and appressoria).
2017-09-26 | PXD002446 | Pride
Project description:Transcriptional changes during asexual sporangia formation by the late blight pathogen Phytophthora infestans were identified using microarrays representing 15,650 genes and RNA from sporulation time-courses, purified spores, and sporulation-defective strains. Results were confirmed by reverse transcription-polymerase chain reaction analyses of sporulation on artificial media and infected tomato. During sporulation, about 12% of genes were found to be up-regulated and 5% down-regulated. The most prevalent induced genes had functions in signal transduction, flagella assembly, cellular organization, metabolism, and molecular or vesicular transport. Distinct patterns of expression were discerned based on the kinetics of mRNA induction and their persistence in sporangia. For example, most flagella-associated transcripts were induced very early in sporulation and maintained in sporangia, while many participants in metabolism or small molecule transport were also induced early but had low levels in sporangia. Data from this study are a resource for understanding sporogenesis, which is critical to the pathogenic success of P. infestans and other oomycetes.
2009-01-27 | GSE13580 | GEO
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:Transcriptional changes during asexual sporangia formation by the late blight pathogen Phytophthora infestans were identified using microarrays representing 15,650 genes and RNA from sporulation time-courses, purified spores, and sporulation-defective strains. Results were confirmed by reverse transcription-polymerase chain reaction analyses of sporulation on artificial media and infected tomato. During sporulation, about 12% of genes were found to be up-regulated and 5% down-regulated. The most prevalent induced genes had functions in signal transduction, flagella assembly, cellular organization, metabolism, and molecular or vesicular transport. Distinct patterns of expression were discerned based on the kinetics of mRNA induction and their persistence in sporangia. For example, most flagella-associated transcripts were induced very early in sporulation and maintained in sporangia, while many participants in metabolism or small molecule transport were also induced early but had low levels in sporangia. Data from this study are a resource for understanding sporogenesis, which is critical to the pathogenic success of P. infestans and other oomycetes. Two arrays were analyzed for each type of biological material. For each of the replicates, RNA was extracted from 2-3 different cultures and pooled. Therefore, a total of 4-6 biological replicates were analyzed for each type of tissue.
2009-01-26 | E-GEOD-13580 | biostudies-arrayexpress
Project description:Within oomycetes, Phytophthora is a genus of eukaryotic microorganisms encompassing some of the most damaging plant pathogens. It spreads by airborne sporangia or waterborne zoospores. Zoospores perceive plant signals through chemotaxis and electrotaxis, and produce signals to attract other zoospores (autotaxis), resulting in auto-aggregation or biofilm formation on the plant surface. The mechanisms underlying intercellular communication and consequent attraction, adhesion and aggregation are largely unknown. Recent studies demonstrated that in Phytophthora parasitica the perception of K+ gradient induced coordinated motion and rapid aggregation. Based on this model, we combined data mining and ultrastructural microscopy analyses to propose a first definition of molecular events leading to oomycete aggregation. Results indicate that the transcriptome repertoire required for aggregation is fully functional already at this single zoospore stage, before aggregation or encystment. Freely swimming zoospores secrete or harbor proteins implied in aggregation through adhesion and extracellular matrix elaboration. They secrete vesicular and fibrillary material, including fibronectin-like proteins, resulting in intercellular structure formation. Consistently, the signature of transcriptome dynamics during transition from single-cell to aggregate is an upregulation of genes contributing to vesicular trafficking, possibly involved in adhesive proteins and extracellular matrix components mobilization. Moreover, the transcriptome signature suggests that pH homeostasis may contribute to aggregation by acting on both zoospore movement and adhesion.
2020-08-12 | GSE142435 | 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:Total RNA extracted from Phytophthora sojae (strain P6497) and infected soybean hypocotyls (cultivar Harosoy) provided template for synthesis of cDNA probes used in the microarray hybridizations. Infected plant hypocotyls were sampled 6 h, 12 h, 24 h, and 48 h after inoculation. Mycelia were grown on synthetic media (H&S) or vegetable juice media (V8). Zoospores were sampled at 0 h, 2 h and 6 h after inducing encystment and germination by agitation. We used microarrays to characterize gene expression patterns in the root rot pathogen Phytophthora sojae and its host Glycine max. Keywords: infection time course, zoospore germination time course, media formulation response
2009-06-22 | GSE15100 | 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
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: In order 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 whose levels are elevated during infection of P. infestans on potato.
2014-12-12 | GSE62674 | GEO