Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Triticum aestivum Transcriptome or Gene expression

ABSTRACT: Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs) were analyzed in wheat callus cells co-cultured with Agrobacterium by using RNA sequencing (RNA-seq). Note: All samples in SRA were assigned the same sample accession (SRS417803). 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Triticum aestivum

SUBMITTER: Xingguo Ye

PROVIDER: E-MTAB-4272 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global analysis of differentially expressed genes and proteins in the wheat callus infected by Agrobacterium tumefaciens.

Zhou Xiaohong X Wang Ke K Lv Dongwen D Lv Dongwen D Wu Chengjun C Li Jiarui J Zhao Pei P Lin Zhishan Z Du Lipu L Yan Yueming Y Ye Xingguo X

PloS one 20131120 11

Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were analyzed in wheat callus cells co-cultured with Agrobacteri ...[more]

PMID: 24278131

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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

Triticum aestivum Transcriptome or Gene expression

Publications

Global analysis of differentially expressed genes and proteins in the wheat callus infected by Agrobacterium tumefaciens.

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