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Phytophthora sojae strain:P6497

ABSTRACT: RNA-seq for Phytophthora sojae and/or Glycine max

PROVIDER: PRJNA396467 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30326704_1.fastq.gz	Fastqsanger.gz
	SRR30326704_2.fastq.gz	Fastqsanger.gz
	SRR30326705_1.fastq.gz	Fastqsanger.gz
	SRR30326705_2.fastq.gz	Fastqsanger.gz
	SRR30326706_1.fastq.gz	Fastqsanger.gz

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Host and pathogen gene expression during early infection of soybean seedlings by Phytophthora sojae, analyzed by ABI Solid RNA sequencing

Project description:Hypocotyls of soybean (Glycine max) seedlings of cultivar Williams were inoculated with mycelia of the oomycete pathogen Phytophthora sojae grown in liquid V8 medium or the hypocotyls were mock inoculated. After 12 hours, the sites of inoculation were excised from the hypocotyls and frozen for RNA extraction. Phytophthora sojae mycelia used for inoculation was saved for RNA extraction also

2021-08-28 | GSE182773 | GEO

ChIP-seq of phytophthora sojae P6497

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.

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Gene expression in Phytophthora sojae mycelia, germinating zoospores, and during infection of soybean hypocotyls

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

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Phytophthora sojae strain:P6497

Project description:RNA-seq reads of Phytophthora sojae Wildtype and PsMAD1 mutants

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Transcriptomes of pssu(z)12 mutant from phytophthora sojae P6497 at mycelium stage

Project description:Purpose and methods:Transcriptome profiling of Phytophthora sojae pssu(z)12 mutant T34 (lost 561bp by CRISPR/Cas9) mycelium (3-days old) were generated to find out the relationship between H3K27me3 and gene expression on Avr1b locus. Wild-type P. sojae P6497 was took as a comparative control. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiles were displayed using IGV browser.

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Gene expression in Phytophthora sojae mycelia, germinating zoospores, and during infection of soybean hypocotyls

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H3K27me3 in Phytophthora sojae P6497 and its pssu(z)12 mutant at mycelium stage

Project description:We report the H3K27me3 profile on Avr1b locus in two Phytophthora sojae strains P6497 and pssu(z)12 mutant. Nuclei of Phytophthora sojae P6497 and pssu(z)12 mutant T34 (lost 561bp by CRISPR/Cas9) mycelium (3-days old) was extracted and digested to 200-400bp using micrococcal nuclease (MNase: NEB M0247S). The antibody Millipore 07-449 was used to immunoprecipitation. We find significant accumulation of H3K27me3 at Avr1b locus in Avr1b silencing strain P6497 and clear H3K27me3 depletion at Avr1b locus in Avr1b unsilenced strain pssu(z)12 mutant T34.

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Phytophthora sojae strain:P6497

Project description:Phytophthora sojae strain:P6497 Raw sequence reads

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Phytophthora sojae strain:P6497

Project description:Phytophthora sojae strain:P6497 Genome sequencing and assembly

| PRJNA563922 | ENA