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Digital gene expression profiling of the Phytophthora sojae transcriptome

ABSTRACT: Digital gene expression profiling of the Phytophthora sojae transcriptome

PROVIDER: PRJNA141239 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR243565.fastq.gz	Fastqsanger.gz
	SRR243566.fastq.gz	Fastqsanger.gz
	SRR243567.fastq.gz	Fastqsanger.gz
	SRR243568.fastq.gz	Fastqsanger.gz
	SRR243569.fastq.gz	Fastqsanger.gz

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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

Digital gene expression profiling of the Phytophthora sojae transcriptome

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.

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Digital gene expression profiling of the Phytophthora sojae transcriptome

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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.

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