Ontology highlight
ABSTRACT:
PROVIDER: PRJNA973852 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24631601_1.fastq.gz | Fastqsanger.gz | |||
| SRR24631601_2.fastq.gz | Fastqsanger.gz | |||
| SRR24631602_1.fastq.gz | Fastqsanger.gz | |||
| SRR24631602_2.fastq.gz | Fastqsanger.gz | |||
| SRR24631603_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Phosphorus, in its orthophosphate form (Pi), 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 Pi deficiency remain largely unknown. White lupin (Lupinus albus L.) has evolved unique adaptations for growth in Pi 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 Pi supply. We de novo assembled 277,224,180 Illumina reads from 12 cDNA libraries to build 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 (RPKM = 3) representing approximately 7.8% of the Lupinus albus 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 Pi deficiency with a = 2-fold change and a p-value = 0.05. Twelve sequences were consistently differentially expressed due to Pi deficiency stress in three species, making them ideal candidates to monitor the Pi status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in Pi deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to Pi deficiency. 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).
2012-11-29 | E-GEOD-31132 | biostudies-arrayexpress
Project description: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.
2012-11-29 | GSE31132 | GEO
Project description:Iron (Fe) and phosphorus (P) are essential nutrients for plants growth. Despite their abundance in soils, they are barely available for plants. In order to overcome these nutritional stresses, plants have evolved strategies including physiological, biochemical and morphological adaptations. Biosynthesis and release of low molecular weight compounds from the roots play a crucial role in P and Fe mobilization. White lupin (Lupinus albus L.) is considered a model plant for studying root exudates and for P-deficient adaptation. White lupin is able to markedly modify its root architecture by forming special structures called cluster roots, and modifies the rhizospheric soil characteristics by biosynthesising and releasing great amounts of exudates. These phenomena are quite well described in response to P deficiency, but there is few information on the adaptation of a cluster-root producing plant species to Fe deficiency. This prompted this work, aimed to characterize the physiological and transcriptomic responses of white lupin plants to Fe deficiency. Occurrence of Strategy I components and interactions with P nutrition has been also investigated in this work. Results showed a physiological and transcriptional link between the responses to Fe and P deficiency in white lupin roots. Phosphorus-deficient plants activated the Strategy I Fe acquisition mechanisms that lead to an enhanced Fe mobilization and translocation and that might help the P acquisition process. On the other hand, also the Fe deficiency enhanced the phosphate acquisition and some P-deficient-responsive genes were overexpressed.
2019-03-22 | GSE112220 | GEO
Project description:RNA-seq analysis of cluster root development in white lupin
| PRJNA241146 | ENA
Project description:This dataset belongs to a set of three RNA-Seq experiments that were carried out to study the regulation of monoterpenoid indole alkaloid production in the medicinal plant Catharanthus roseus. For this dataset, C. roseus hairy roots overexpressing the well-known MIA biosynthesis regulator ORCA3 were analyzed by RNA-Seq. As control, C. roseus hairy roots expressing GUS were used. Each analyzed sample consisted of an independent hairy root line; three hairy root lines per construct were analyzed.
2020-09-07 | E-MTAB-9514 | biostudies-arrayexpress
Project description:RNA sequencing was performed on tomato hairy root lines transformed with a GUS overexpression construct, 24 h after mock and jasmonate (JA) treatment. This set-up allowed us to map the gene targets of JA in tomato hairy roots after 24h.
2022-07-08 | E-MTAB-11876 | biostudies-arrayexpress
Project description:We identified two novel transcription factors ‘Triterpene Saponin Activation Regulator’ (TSAR) 1 and 2 that each activate a specific branch of saponin synthesis in M. truncatula. Therefore we generated three independent TSAR1 and three independent TSAR2 overexpression (OE) hairy root lines. As a control we raised three independent hairy root lines expressing a non-functional GUS gene. By qRT-PCR analyses and metabolite profiling of these lines, we found that TSAR1 OE leads to accumulation of non-haemolytic saponins whereas TSAR2 instigates accumulation of haemolytic saponins. To identify additional targets of TSAR1 and TSAR2 we carried out a genome-wide transcript profiling study by RNA-Seq.
2017-02-15 | E-MTAB-3532 | biostudies-arrayexpress
Project description:To investigate the effect of overexpression of wild-type and kinase deactivated GmBIR1 on soybean transgenic hairy root gene expression
2023-05-31 | GSE220163 | GEO
Project description:Phosphorus (P) and iron (Fe) deficiency are major limiting factors for plant productivity worldwide. White lupin (Lupinus albus L.) has become a model plant for understanding plant adaptations to P and Fe deficiency, because of its ability to form cluster roots, bottle-brush-like root structures that play an important role in the uptake of P and Fe from soil. However, little is known about the signaling pathways involved in sensing and responding to P and Fe deficiency. Sucrose, sent in increased concentrations from the shoot to the root, has been identified as a long- distance signal of P and Fe deficiencies. To unravel responses to sucrose as a signal, we performed Oxford Nanopore cDNA sequencing of white lupin roots treated with sucrose for 10 min, 15 min, and 20 min, compared to untreated controls. We identified a set of 17 genes, including two bHLH transcription factors, that were upregulated at all three time points of sucrose treatment. GO (gene ontology) analysis revealed enrichment of auxin- and gibberellin-responses as early as 10 min after sucrose addition, and the emerging of ethanol-responses at 20 min of sucrose treatment, indicating a sequential involvement of these hormones in plant responses to sucrose.
2024-05-27 | GSE268152 | GEO