Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Oryza sativa Japonica Group transcriptome sequencing

ABSTRACT: Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Youko Matsumoto

PROVIDER: E-MTAB-4302 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Rice has developed several morphological and physiological strategies to adapt to phosphate starvation stress. In order to elucidate the molecular bases of response due to phosphate stress particularly the transcriptional profile of genotypes with variation in tolerance to phosphate starvation, we analyzed the gene expression profiles of 3 japonica rice cultivars and an indica cultivar with different levels of tolerance to phosphate starvation using the RNA-Seq method. We constructed a total of 48 libraries corresponding to root and shoot of the 4 cultivars for control (0 d) and âP treatment (22 d) with three biological replicates for root and shoot samples in each cultivar. Approximately 254 million sequenced tags were mapped onto the reference rice genome sequence (IRGSP1.0) and an average of about 5,000 transcripts in each genotype were found to be responsive to Pi-starvation. Comparative analysis of the responsive transcripts revealed an overall similarity in the transcriptome signatures resulting from phosphate starvation as well as distinct differences that distinguish the degree of tolerance among the 4 cultivars. We elucidated a set of core responsive transcripts commonly expressed in both root and shoot with different levels of expression reflecting variation as well genotype specificity in tolerance to Pi-starvation. De novo assembly of unmapped reads generated a large set of sequence assemblies that represent potential new transcripts that may be involved in tolerance to phosphate deficiency. Characterization of 88 assemblies unaligned in the reference genome revealed several dozen transcripts which correspond to plant ESTs. This study provides an overview of the diversity in response to P-starvation stress that can be used to identify the major genes for improving Pi acquisition and utilization in rice and other cereal crops. Note: Samples in DRA 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 DRA sample accessions.

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.

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Oryza sativa Japonica Group transcriptome sequencing

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