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Phytophthora sojae

ABSTRACT: Phytophthora sojae Raw sequence reads

PROVIDER: PRJNA832871 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR19018800_1.fastq.gz	Fastqsanger.gz
	SRR19018800_2.fastq.gz	Fastqsanger.gz
	SRR19018801_1.fastq.gz	Fastqsanger.gz
	SRR19018801_2.fastq.gz	Fastqsanger.gz
	SRR19018802_1.fastq.gz	Fastqsanger.gz

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Phytophthora sojae

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Digital gene expression profiling of the Phytophthora sojae transcriptome

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

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.

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Phytophthora sojae strain:P6497

Project description:Phytophthora sojae strain:P6497 Raw sequence reads

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Phytophthora sojae strain:6497

Project description:Phytophthora sojae strain:6497 Raw sequence reads

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Phytophthora sojae strain:sc10

Project description:Phytophthora sojae strain:sc10 Raw sequence reads

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Phytophthora sojae cultivar:P6497

Project description:Phytophthora sojae cultivar:P6497 Raw sequence reads

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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 sojae strain:P6497

Project description:Phytophthora sojae Raw sequence reads from four developmental stages

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