Ontology highlight
ABSTRACT:
PROVIDER: PRJNA953600 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24121410.fastq.gz | Fastqsanger.gz | |||
| SRR24121411_1.fastq.gz | Fastqsanger.gz | |||
| SRR24121411_2.fastq.gz | Fastqsanger.gz | |||
| SRR24121412_1.fastq.gz | Fastqsanger.gz | |||
| SRR24121412_2.fastq.gz | Fastqsanger.gz |
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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: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
Project description:During germination and early seedling development plants rely entirely on their seed storage compounds to provide energy and precursors for the synthesis of macromolecular structures such as cell walls until the seedling has emerged from the soil and photosynthesis can be established. Lupin seeds use proteins as their major storage compounds, accounting for up to 40% of the seed dry weight. Lupins are therefore a valuable complement to soy as a source of plant protein for human and animal nutrition. However, knowledge on protein and amino acid metabolism during germination and seedling establishment in lupin plants is still limited. The aim of this study was to elucidate how storage protein metabolism is coordinated with other metabolic processes to meet the requirements of the growing seedling. In a quantitative approach, we analyzed seedling growth, as well as alterations in biomass composition, the proteome, and metabolite profiles during germination and seedling establishment in Lupinus albus. The reallocation of nitrogen resources from seed storage proteins to functional seed proteins was mapped based on a manually curated functional protein annotation database. Although classified as a protein crop, Lupinus albus does not use amino acids as a primary resource during germination. The predominant role of the stored proteins is to act as a nitrogen resource for vigorous post-germinative growth. The degradation of storage lipids and carbohydrates is sufficient to meet the energy requirements for early seedling establishment until the onset of photosynthesis. However, our results suggest that during germination fatty acid and amino acid metabolism may be integrated at the level of malate synthase to combine stored carbon from lipids and proteins into gluconeogenesis.
2024-07-26 | PXD046789 | Pride
Project description:RNA-seq analysis was performed on different developmental stages of cluster roots (pre-emergent, juvenile and mature) from Lupinus albus grown for 20 days under phosphorus-deficiency
2014-07-01 | E-MTAB-2253 | biostudies-arrayexpress
Project description:Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organization of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment. In order gain a better understanding of the epigenetic organization of genomes in lupins we applied the immunostaining of methylated histone H3 and DNA methylation as well as whole-genome bisulfite sequencing. We revealed variations in the patterns of chromatin modifications at the chromosomal level among three crop lupins, i.e. L. angustifolius (2n=40), L. albus (2n=50) and L. luteus (2n=52), and the legume model plant Medicago truncatula (2n=16). Different chromosomal patterns were found depending on the specific modification, e.g. H3K4me2 was localised in the terminal parts of L. angustifolius and M. truncatula chromosomes, which is in agreement with the results that have been obtained for other species. Interestingly, in L. albus and L. luteus this modification was limited to one arm in the case of all of the chromosomes in the complement. Additionally, H3K9me2 was detected in all of the analysed species except L. luteus. DNA methylation sequencing (CG, CHG and CHH contexts) of aforementioned crop but also wild lupins such as L. cosentinii (2n=32), L. digitatus (2n=36), L. micranthus (2n=52) and L. pilosus (2n=42) supported the range of interspecific diversity. The examples of epigenetic modifications illustrate the diversity of lupin genomes and could be helpful for elucidating further epigenetic changes in the evolution of the lupin genome.
2017-08-17 | GSE98637 | GEO
Project description:Arsenic stress triggers active exudation of arsenic-phytochelatin complexes from Lupinus albus roots
2023-10-10 | MSV000093078 | MassIVE
Project description:Obtaining large amounts of protein of plant origin is an indispensable prospect from the perspective of environmental changes taking place on earth. However, it is extremely important to be able to diversify the sources of plant proteins, which is affected, among other things, by their local availability, sensitivity to specific climatic conditions of the region, and the qualitative differentiation of amino acids. A lot of data show that higher amounts of protein with improved properties can be obtained from species native to a specific climate zone. In Europe, such species include yellow lupine (Lupinus luteus L.), narrow-leaved lupine (Lupinus angustifolius) and white lupine (Lupinus albus L.). In the case of yellow lupine, the amount may be up to 40% of the dry weight of the seeds. Additionally, these proteins have a favorable amino acid composition. Detailed understanding of the mechanisms and the process of accumulating storage proteins is invaluable for the study of the use of this species to increase the production of plant proteins. In the presented work, yellow lupine seeds cultivar Taper, which were cultivated in the field, were used for the research. Therefore, the aim of the research was to identify genes encoding storage proteins (conglutins) and genes regulating the process of accumulation of storage proteins in the seeds of yellow lupine cultivar Taper in the following days of their development.
2023-08-21 | GSE207091 | GEO