Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Time-course transcriptome analysis of mature nodules in Medicago truncatula grown in split-root under different nitrogen (N) supply

ABSTRACT: The experiment aim is the identification of the transcriptional response of mature nodules of Medicago truncatula inoculated with the strain MD4 of Sinorhizobium medicae in response to different nitrogen (N) supply (N-satiety and N-deficient conditions). We performed a time-course (1 and 3 days treatment) split-root experiment to identify plant systemic responses: the root systems of nodulated symbiotic plants were divided into two compartments, one of them treated and the other kept on control conditions. Nodules were isolated from the non-treated side of the split root and total RNA isolated for RNAseq analysis.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Medicago truncatula

SUBMITTER: Ilana Lambert

PROVIDER: E-MTAB-8597 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Responses of mature symbiotic nodules to the whole-plant systemic nitrogen signaling.

Lambert Ilana I Pervent Marjorie M Le Queré Antoine A Clément Gilles G Tauzin Marc M Severac Dany D Benezech Claire C Tillard Pascal P Martin-Magniette Marie-Laure ML Colella Stefano S Lepetit Marc M

Journal of experimental botany 20200801 16

In symbiotic root nodules of legumes, terminally differentiated rhizobia fix atmospheric N2 producing an NH4+ influx that is assimilated by the plant. The plant, in return, provides photosynthates that fuel the symbiotic nitrogen acquisition. Mechanisms responsible for the adjustment of the symbiotic capacity to the plant N demand remain poorly understood. We have investigated the role of systemic signaling of whole-plant N demand on the mature N2-fixing nodules of the model symbiotic associatio ...[more]

PMID: 32386062

Similar Datasets

Effect of the sunn mutation on systemic signalling of the plant N demand in Medicago truncatula plants inoculated for 2 or 7 days with Sinorhizobium medicae

Project description:The experiment aims to investigate the effect of the sunn mutation on systemic signaling of the plant N demand in Medicago truncatula roots inoculated with Sinorhizobium medicae MD4 at 2 and 7 days post-inoculation (dpi). We compared the TR122/sunn-2 mutant to the wild type Jemalong A17. For each plant genotype, we divided the roots systems into two parts; one of them was supplied with a nutrient solution with mineral N (10 mM NH4NO3 for N-satisfied plants, 0.5 mM for N-limited plants) whereas the non-N treated part was kept in a nutrient solution without mineral N. All roots were inoculated 48h after initiation of the N treatments. To characterize specifically the impact of systemic signaling of N demand, we collected for both genotypes the roots of the non-N treated sides of the split roots systems, and we isolated total RNA for RNAseq analysis. Root transcriptomes of N-limited and N-satisfied plants were compared in both genotypes at 2 or 7 dpi.

2021-04-30 | E-MTAB-9942 | biostudies-arrayexpress

Time-course transcriptome analysis of Sinorhizobium medicae (MD4 strain) in mature nodules of Medicago truncatula grown in split-root under different nitrogen (N) supply

Project description:The experiment aim is the identification of the transcriptional response of mature nodules of Medicago truncatula inoculated with the strain MD4 of Sinorhizobium medicae in response to different nitrogen (N) supply (N-satiety and N-deficient conditions). We performed a time-course (1 and 3 days treatment) split-root experiment to identify plant systemic responses: the root systems of nodulated symbiotic plants were divided into two compartments, one of them treated and the other kept on control conditions. Nodules were isolated from the non-treated side of the split root and total RNA isolated for RNAseq analysis. To analyse Sinorhizobium medicae MD4 expression, a ribosomal RNA depletion protocol was performed before library preparation.

2020-09-30 | E-MTAB-8598 | biostudies-arrayexpress

Effect of contrasted N regimes on the root transcriptome of Medicago truncatula plants cultivated in split root systems and inoculated for 2, 4 and 7 days with Sinorhizobium medicae

Project description:The experiment aims to analyze the effect of systemic signaling of plant N demand on the transcriptome of Medicago truncatula roots inoculated with Sinorhizobium medicae MD4 at 2, 4, and 7 days post-inoculation (dpi). We divided the roots systems into two parts; one of them was supplied with nutrient solution with mineral N (10 mM NH4NO3 for N-satisfied plants, 0.5 mM for N-limited plants) whereas the non-N treated part was kept in nutrient solution without mineral N. All roots were inoculated 48h after initiation of the N treatments. To characterize specifically the impact of systemic signaling of N demand, we collected the roots the non-N treated sides of the split roots systems and we isolated total RNA for RNAseq analysis. Root transcriptomes of N-limited and N-satisfied plants were compared at 2, 4 and 7 dpi.

2021-04-30 | E-MTAB-9941 | biostudies-arrayexpress

Time-course transcriptome analysis in roots of N-limited Medicago truncatula plants grown in split-root inoculated with Sinorhizobium medicae

Project description:The experiment aims to analyze the effect of inoculation with Sinorhizobium medicae MD4 of on the transcriptome of the Medicago truncatula roots of N-limited plants. We divided the roots systems into two parts; one of them was supplied with nutrient solution with mineral N (0.5 mM for N-limited plants) whereas the non-N treated part was kept in nutrient solution without mineral N. All roots were inoculated 48h after initiation of the N treatments. We collected the roots the non-N treated side of the split roots system and we isolated total RNA for RNAseq analysis. Root transcriptomes were analyze before inoculation, at 1 and 2 days post-inoculation.

2021-04-30 | E-MTAB-9932 | biostudies-arrayexpress

Response of the mature nodules and denodulated roots of the Medicago truncatula/sinorhizobium medicae md4 symbiotic association to systemic signaling of plant N deficit

Project description:The experiment aims to identify the response of mature nodules and denodulated roots of Medicago truncatula /Sinorhizobium medicae md4 to the systemic signaling of plant N deficit. The root systems of nodulated symbiotic plants were divided into two compartments. The N source of N2 fixing plants was exclusively the air. To reduce the plant nitrogen (N) supply (N-deficient conditions), we flushed one half root system with Ar/O2 (80/20 v/v) while the other half root system was kept on control conditions (Air). To characterize the systemic responses of the transcriptome to plant N deficit , nodules and roots of the non-treated half root system were harvested and total RNA isolated for RNAseq analysis. We performed a time-course (6 hours, 1-, 3- and 5-days treatment).

2021-11-30 | E-MTAB-10496 | biostudies-arrayexpress

Response of the mature nodules of the Medicago truncatula/sinorhizobium medicae md4 symbiotic association to systemic signaling associated to plant water deficit (PEG treatment)

Project description:The experiment aims to identify the response of the mature nodules and denodulated roots of Medicago truncatula /Sinorhizobium medicae md4 to the systemic signaling of plant water deficit. The root systems of nodulated symbiotic plants were divided into two compartments. The N source of N2 fixing plants was exclusively the air. To apply the water stress, we treated half root system with PEG while the other was kept on control conditions. To characterize the systemic responses of the transcriptome to the PEG treatment , nodules and roots of the non-treated half root system were harvested and total RNA isolated for RNAseq analysis. We performed a time-course (6 hours, 1-, 3- and 5-days treatment) .

2021-11-30 | E-MTAB-10497 | biostudies-arrayexpress

Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies

Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.

2016-10-10 | PXD004039 | Pride

Transcriptional response of durum wheat roots and leaves to continuous chromium stress

Project description:Chromium (Cr) is a highly toxic heavy metal for both mono and dicot plants, causing severe cellular damage and disturbances in plant growth, development, and reproduction. Its phytotoxicity results in serious changes in plant physiology, gene expression, and at a transgenerational level in genomic DNA methylation. Herein, transcriptional responses of durum wheat (Triticum turgidum L.) to continuous and basal Cr stress were explored in roots and leaves by RNAseq analysis. Plants cultivated in a hydroponic system supplemented with 2.5 and 10 µM Cr were compared with control plants through transcriptomic analysis after 50 days and for the biomass accumulation and seed yield after senescence.

2024-08-26 | E-MTAB-13952 | biostudies-arrayexpress

Transcriptional response in leaves and root of potato plants to cadmium (Cd) exposure

Project description:Study transcriptional response in potato to cadmium exposure.

2020-01-01 | E-MTAB-7711 | biostudies-arrayexpress

Characterization of two urea-utilizing pathways in coral reef ecosystems: implications for the significance of the urea cycle in facing global warming

Project description:Urea can serve as nitrogen source for coral holobionts and plays a cruscial role in coral calcification, although the degradation of urea by coral symbionts is not fully understood. In this study, we investigated the urea utilized pathway and the responses of the Symbiodiniaceae family to urea under high temperature conditions. Genome screening revealed that all Symbiodiniaceae species contain the urease (URE) and DUR2 subunit of urea amidolyase (UAD) system. However, only three speciesCladocopium goreaui, Cladopium c92, and Symbiodinium pilosum possess a complete UAD system, including both DUR1 and DUR2. Phylogentic analyses revealed that the UAD system in Symbiodiniaceae clusters more closely with symbiotic bacteria, indicating that horizontal gene transfer of UAD system has occured in coral symbionts. Physiology analysis showed that the symbiodiniacean species Cladocopium goreaui, which containing both URE and UAD, grew better under urea than ammonium conditions, as indicated by higher maximum specific growth rates. Furthermore, most genes of Symbiodiniaceae involved in urea utilization appeared to be stable under various conditions such as heat stress (HS), low light density, and nitrogen deficiency, wheras in ammonium and nitrate transporters were significantly regulated. These relatively stable molecular regulatory properties support sustained urea absorption by Symbiodiniaceae, as evidenced by an increase in δ15N2-urea absorption and the decreases in δ5N-NO3-, and δ15N-NH4+ from cultural environment to Symbiodiniaceae under HS conditions. Token together, this study reveals two distinct urea utilization systems in coral ecosystem and highlights the importance of the urea cycle in coral symbionts when facing fluctuating nitrogen environment in future warming ocean.

2024-09-27 | PXD056312 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data