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Digital gene expression profiling of the Phytophthora sojae transcriptome

ABSTRACT: 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.

ORGANISM(S): Phytophthora sojae

SUBMITTER: Wenwu Ye

PROVIDER: E-MTAB-4039 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Digital gene expression profiling of the Phytophthora sojae transcriptome.

Ye Wenwu W Wang Xiaoli X Tao Kai K Lu Yuping Y Dai Tingting T Dong Suomeng S Dou Daolong D Gijzen Mark M Wang Yuanchao Y

Molecular plant-microbe interactions : MPMI 20111201 12

The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at ten different developmental and infection stages based on a 3'-tag digital gene-expression protocol. More than 90 million clean sequence tags were generated and compared with 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 f ...[more]

PMID: 21848399

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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. The five axenically grown stages were mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY), and germinating cysts (GC). The five infection stages, 1.5, 3, 6, 12 and 24 h after inoculation onto susceptible soybean leaf tissues (IF1.5h to IF24h).

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