Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Oryza sativa strain:CL 161, CL 151 Transcriptome or Gene expression

ABSTRACT: Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a model for rice resistance to the disease. There was a total of 36 tissue samples that included 2 rice genotypes (CL 151 and CL 161) Ã 2 treatment groups (water control and bacterium inoculated) Ã 3 time points Ã 3 biological replicates. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryza sativa

SUBMITTER: Zenaida Magbanua

PROVIDER: E-MTAB-4406 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptomic dissection of the rice-Burkholderia glumae interaction.

Magbanua Zenaida V ZV Arick Mark M Buza Teresia T Hsu Chuan-Yu CY Showmaker Kurt C KC Chouvarine Philippe P Deng Peng P Peterson Daniel G DG Lu Shien S

BMC genomics 20140903

<h4>Background</h4>Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a mo ...[more]

PMID: 25183458

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Project description:Phosphorus (P) is an essential macronutrient for plant growth and development, and a plant must balance P uptake, mobilisation, and partitioning to various organs to modulate P homeostasis. The underlying molecular mechanisms of wheat under phosphate (Pi) starvation conditions remain elusive despite wheat is an important cultivated food crop worldwide. We generated transcriptome profiles of wheat variety Chinese Spring (CS) in response to Pi starvation (-P) for 10 days using RNA-Seq methods.We used 73.8 million high-quality reads obtained from libraries for de novo assembly. Overall, a set containing 29,617 non-redundant wheat transcripts was constructed with 15,047 assemblies and 14,570 non-redundant, full-length cDNAs in TriFLDB. Of the transcripts, 10,656 of the 15,047 assemblies were unaligned against barley full-length cDNAs, suggesting that many of them might be distinct of barley transcripts. The distribution of average expression levels for the assembly was lower than that for cDNAs, suggesting that the assemblies contained rare transcripts limited availability using full-length cDNA library construction methods. Within the transcript set, we identified 892-2,833 up- or downregulated transcripts in root and shoot, including 18.9-40.5% assemblies, uncovered by cDNAs in TriFLDB under -P in each condition. In the results, the expression level of wheat IPS1 (induced by phosphate starvation 1) homolog, TaIPS1, was 358.6-fold higher in the root and 12.6-fold higher in the shoot, which was confirmed by qRT-PCR analysis. Comparative analysis between wheat (a rice orthologue) and rice responsive transcripts under -P conditions showed that 39 (root) and 21 (shoot) responsive transcripts were commonly upregulated, and most of them seemed to be involved in a general response to -P; IPS1-mediated signal transduction and its downstream function such as Pi remobilization, Pi uptake and change metabolism.Our transcriptome profiling demonstrates the impact of -P in wheat. This study shows that enhancing the Pi-mediated signalling pathway through IPS1 is conserved as a potent adaptation to Pi starvation in both wheat and rice, and also that our constructed strategy using short read next generation sequencing (NGS) data was successful for the transcriptome analysis in wheat without reference genome. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

Dataset Information

Oryza sativa strain:CL 161, CL 151 Transcriptome or Gene expression

Publications

Transcriptomic dissection of the rice-Burkholderia glumae interaction.

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