Phytophthora sojae
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ABSTRACT:
PROVIDER: PRJNA127755 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This experiment contains Phytophthora sojae samples and RNA-seq data from experiment E-GEOD-29561 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29651/) to understand gene expression during the P. sojae life cycle. The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 5 different developmental stages: mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY) and germinating cysts (GC); based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established.
2011-09-01 | E-MTAB-4039 | biostudies-arrayexpress
Project description:Examination of soybean hypocotyls, G. max cv. Harosoy (Rps7), at 3, 6, 12, 24 and 48 hours after inoculation with P. sojae, race 2, isolate P6497 Patterns of Gene Expression Upon Infection of Soybean Plants by Phytophthora sojae. P. Moy, D. Qutob, B. P. Chapman, I. Atkinson, and M. Gijzen. Pages 1051-1062. Publication no. M-2004-0728-01R. Molecular Plant-Microbe Interactions, October 2004, Volume 17, Number 10. Keywords: time-course
2004-09-14 | GSE1352 | GEO
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:To identify soybean genes and QTLs associated with quantitative resistance to infection by the oomycete pathogen Phytophthora sojae, we conducted a very large-scale microarray experiment using 2522 Affymetrix GeneChips. The experiment involved assaying a total of 298 soybean recombinant inbred lines together with internal checks.
2008-05-30 | GSE11611 | GEO
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 28 samples from 9 treatments; 2 to 5 biological replicates per treatment.
2009-06-22 | E-GEOD-15100 | biostudies-arrayexpress
Project description:Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromeric sequences are diverse and usually repetitive across species, making them challenging to assemble and identify. Here, we describe centromeres in the model oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus in the nucleus at different life stages and during nuclear division. We report a highly contiguous genome assembly of the P. sojae reference strain, which enabled identification of 15 highly enriched CENP-A binding regions as putative centromeres. By focusing on 10 intact regions, we demonstrate that centromeres in P. sojae are regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, and lack the euchromatin mark H3K4me2 but are embedded within regions with the heterochromatin marks H3K9me3 and H3K27me3.
2020-01-07 | GSE143137 | GEO
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 sojae mycelium small RNAs were sequenced and aligned to the P. sojae genome for analysis. *Raw data files (fastq) are unavailable for this study.
2013-10-21 | E-GEOD-50032 | biostudies-arrayexpress
Project description:The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 10 different developmental and infection stages based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A comparison of the whole-library genes expression patterns suggested four groups: 1) mycelia and zoosporangia (MY and SP); 2) zoospores and cysts (ZO and CY); 3) germinating cysts (GC); 4) five infection site libraries (IF1.5 to IF24h). The libraries from the different groups showed major transitional shifts in gene expression. From the ten libraries, 722 gene expression pattern clusters were obtained and the top 16 ones, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and non-coding RNA metabolism. An evaluation of the average expression level of 30 pathogenesis related gene families revealed that most were infection induced, but with diverse expression patterns and levels. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established.
2011-09-01 | GSE29651 | GEO
Project description:Plant pathogens secreted effector proteins to overcome host immunity system and gain access to colonization. Although more than 300 hundred of RxLR effectors were encoded by the devastating soybean pathogen Phytophthora sojae, the patterns of conditionally expressed effector genes were well programmed. However, the effector gene regulation mechanisms were not fully dissected. In this study, we identified the H3K36me3 methyltransferase PsKMT3. Phenotypic assays showed PsKMT3 was involved in regulation of growth, sporulation, zoospore production and pathogenicity. ChIP-seq analysis, together with RNA-seq analysis, showed PsKMT3 controlled a set of RxLR gene expression. The transcriptome comparison showed large-scale mis-expression of RxLR waves during mycelium, 3 hpi and 6 hpi stages between WT and pskmt3. Our result supports a new RxLR gene regulation mechanisms in which methyltransferase PsKMT3 maintains well programmed RxLR gene expression in P. sojae.
2023-03-22 | GSE205360 | GEO
Project description:Plant pathogens secreted effector proteins to overcome host immunity system and gain access to colonization. Although more than 300 hundred of RxLR effectors were encoded by the devastating soybean pathogen Phytophthora sojae, the patterns of conditionally expressed effector genes were well programmed. However, the effector gene regulation mechanisms were not fully dissected. In this study, we identified the H3K36me3 methyltransferase PsKMT3. Phenotypic assays showed PsKMT3 was involved in regulation of growth, sporulation, zoospore production and pathogenicity. ChIP-seq analysis, together with RNA-seq analysis, showed PsKMT3 controlled a set of RxLR gene expression. The transcriptome comparison showed large-scale mis-expression of RxLR waves during mycelium, 3 hpi and 6 hpi stages between WT and pskmt3. Our result supports a new RxLR gene regulation mechanisms in which methyltransferase PsKMT3 maintains well programmed RxLR gene expression in P. sojae.
2023-03-22 | GSE205359 | GEO