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Phytophthora sojae

ABSTRACT: Small RNA sequencing of P. sojae strains and progeny

PROVIDER: PRJNA300858 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2915320.fastq.gz	Fastqsanger.gz
	SRR2915311.fastq.gz	Fastqsanger.gz
	SRR2915321.fastq.gz	Fastqsanger.gz
	SRR2915331.fastq.gz	Fastqsanger.gz
	SRR2915312.fastq.gz	Fastqsanger.gz

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Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora sojae small RNA

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

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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Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora sojae small RNA

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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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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.

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