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| Status |
Public on Nov 29, 2012 |
| Title |
An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants |
| Organism |
Lupinus albus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Phosphorus, in its orthophosphate form (P(i)), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to P(i) deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in P(i)-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to P(i) supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to P(i) deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to P(i) deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the P(i) status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in P(i) deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to P(i) deficiency.
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| Overall design |
Examination of 2 different tissue types (roots and leaves) under phosphorus (P) -sufficient or P-deficient condition with 3 biological replications per condition in white lupin (Lupinus albus).
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| Contributor(s) |
Yang SS, Vance CP, O'Rourke J |
| Citation(s) |
23197803 |
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| Submission date |
Aug 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Sam Yang |
| E-mail(s) |
yangsh38@hotmail.com
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| Phone |
612-626-6582
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| Organization name |
USDA
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| Department |
ARS
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| Lab |
Carroll Vance
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| Street address |
411 Upper Buford Circle
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| City |
St Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
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| Platforms (1) |
| GPL14013 |
Illumina Genome Analyzer IIx (Lupinus albus) |
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| Samples (12)
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| GSM770773 |
Roots phosphorous deficient rep1 PdR1 |
| GSM770774 |
Roots phosphorous deficient rep2 PdR2 |
| GSM770775 |
Roots phosphorous deficient rep3 PdR3 |
| GSM770776 |
Roots phosphorous sufficient rep1 PsR1 |
| GSM770777 |
Roots phosphorous sufficient rep2 PsR2 |
| GSM770778 |
Roots phosphorous sufficient rep3 PsR3 |
| GSM770779 |
Leaves phosphorous deficient rep1 PdL1 |
| GSM770780 |
Leaves phosphorous deficient rep2 PdL2 |
| GSM770781 |
Leaves phosphorous deficient rep3 PdL3 |
| GSM770782 |
Leaves phosphorous sufficient rep1 PsL1 |
| GSM770783 |
Leaves phosphorous sufficient rep2 PsL2 |
| GSM770784 |
Leaves phosphorous sufficient rep3 PsL3 |
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| Relations |
| SRA |
SRP007642 |
| BioProject |
PRJNA144943 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31132_Digital_Gene_Expression_Profile_Matrix.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE31132_LAGI1.0.fasta.gz |
42.6 Mb |
(ftp)(http) |
FASTA |
| GSE31132_LAGI1.0_Annotation.txt.gz |
5.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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