home > bioproject > PRJDB2496
identifier PRJDB2496
type bioproject
sameAs
sra-study  DRP000768
organism Triticum aestivum
title Characterisation of the wheat (Triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes
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.
data type DDBJ SRA Study
publication
23379779
external link
properties 
{...}
dbXrefs
sra-run  DRR003148DRR003149DRR003150DRR003151DRR003152DRR003153DRR003154DRR003155DRR003156DRR003157 More
sra-submission  DRA000737
biosample  SAMD00012314SAMD00012311SAMD00012313SAMD00012312
sra-study  DRP000768
sra-sample  DRS002575DRS002576DRS002577DRS002578
sra-experiment  DRX002485DRX002486DRX002487DRX002488DRX002489DRX002490DRX002491DRX002492DRX002493DRX002494 More
distribution JSONJSON-LD
status public
visibility unrestricted-access
dateCreated 2014-05-12T00:46:27+0000
dateModified 2014-05-12T00:46:27+0000
datePublished 2014-05-12T00:46:27+0000