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Metabolite Profiling Experiments

The GC-MS metabolite profiling experiments given below are made publicly available to get feedback from the community. The relative metabolite concentrations are normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol). Although these details are accessible within the GMD, they are not made available on the web site so far. For these details please refer to the publication. As it is our intention to increase the breadth GMD’s experiment repository in terms of organisms, organs and stresses, we actively work on cross experiment normalisation and thus, profile data and data representation might change in the future without any further notice. For maximal quality assessment, all experiments are described using the XEML framework (see tree below), while the GC-MS chromatograms are processed using the TagFinder software.
Title
Factor(s)GenusAccessionsReplica GroupsSamplesMetabolites
Metabolomic responses to long-term salt stress in related Lotus species (C)
Germplasm, SaltLotus8168459
15 experiment(s)
Metabolomic responses to long-term salt stress in related Lotus species (C) contact: kopka@mpimp-golm.mpg.de description: The legume genus Lotus includes glycophytic forage crops and other species adapted to extreme environments, such as saline soils. Understanding salt tolerance mechanisms will contribute to the discovery of new traits which may enhance the breeding efforts towards improved performance of legumes in marginal agricultural environments. Here, we used a combination of ionomic and gas chromatography-mass spectrometry (GC-MS)-based metabolite profilings of complete shoots (pooling leaves, petioles and stems) to compare the extremophile Lotus creticus, adapted to highly saline coastal regions, and two cultivated glycophytic grassland forage species, Lotus corniculatus and Lotus tenuis. L. creticus exhibited better survival after exposure to long-term lethal salinity and was more efficient at excluding Cl- from the shoots than the glycophytes. In contrast, Na+ levels were higher in the extremophile under both control and salt stress, a trait often observed in halophytes. Ionomics demonstrated a differential rearrangement of shoot nutrient levels in the extremophile upon salt exposure. Metabolite profiling showed that responses to NaCl in L. creticus shoots were globally similar to those of the glycophytes, providing little evidence for metabolic pre-adaptation to salinity. This study is the first comparing salt acclimation responses between extremophile and non-extremophile legumes, and challenges the generalization of the metabolic salt pre-adaptation hypothesis. start date: 2007-01-01 experiment Id: 747b1c79-3ef5-486f-b5ba-4faf0b0f55e5 links: metabolite profile  MapMan pathway  XEML experimental description  ISA-Tab export  TagList Metabolite raw export  TagList Metabolite norm export  TagList Analyte raw export  TagList Analyte norm export  TagList MST raw export
  • 7311if - Ea27c
  • doi:10.1111/j.1365-3040.2010.02266.x
  • doi:10.1371/journal.pone.0017094
  • Sanchez DH, Pieckenstain FL, Szymanski J, Erban A, Bromke M, et al. (2011) Comparative Functional Genomics of Salt Stress in Related Model and Cultivated Plants Identifies and Overcomes Limitations to Translational Genomics. PLoS ONE 6(2): e17094. doi:10.1371/journal.pone.0017094
  • Sanchez, D. H., Pieckenstain, F. L., Escaray, F., Erban, A., Kraemer, U., Udvardi, M. K. and Kopka, J. (2011), Comparative ionomics and metabolomics in extremophile and glycophytic Lotus species under salt stress challenge the metabolic pre-adaptation hypothesis. Plant, Cell & Environment, 34: 605–617. doi: 10.1111/j.1365-3040.2010.02266.x
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observation point: OP 2 observation time: 32.00:00:00 [days . hours : minutes : seconds]
TimeNameValueDurationUnit
initiationSalt0 mol/l
initiationTypeAgar  
initiationTypeSeeds were germinated on agar plates with half-strength BD solution plus 2 mM KNO3 and 2 mM NH4NO3.  
initiationContainerPetri dish  
04dContainerPot  
04dContainerPot size: 10 cm  
04dWateringPlants were watered with half-strength BD solution plus 2 mM KNO3 and 2 mM NH4NO3.  
04dTypePotting soil  
04dTypeSoil type: Einheit (Type 0)  
04dTemperature23 °C
04dTemperature23+/-2°C  
04dRelativeHumidity60 %
04dRelativeHumidity55-65% RH  
04dTotal Lighton16:00:00 
04dTotal Lightoff08:00:00 
08dSalt50 mol/l
12dSalt100 mol/l
16dSalt150 mol/l
18 experimental conditions(s)
ReplicaGroupLabelGermPlasmMaterialDevelopmental Stage
rg10 Salt:150mol/l Lotus tenuis.La EsmeraldaLotus tenuis.La Esmeraldawhole plant1 main shoot growth stage
rg11 Salt:150mol/l Lotus creticusLotus creticuswhole plant1 main shoot growth stage
rg12 Salt:150mol/l Lotus uliginosus.LE G27Lotus uliginosus.LE G27whole plant1 main shoot growth stage
rg13 Salt:150mol/l Lotus filicaulisLotus filicauliswhole plant1 main shoot growth stage
rg14 Salt:150mol/l Lotus japonicus.MG20Lotus japonicus.MG20whole plant1 main shoot growth stage
rg15 Salt:150mol/l Lotus burtii.B303Lotus burtii.B303whole plant1 main shoot growth stage
rg16 Salt:150mol/l Lotus japonicus.Gifu B129Lotus japonicus.Gifu B129whole plant1 main shoot growth stage
rg9 Salt:150mol/l Lotus corniculatus.San GabrielLotus corniculatus.San Gabrielwhole plant1 main shoot growth stage
8 replica group(s)
This tree schematises the experimental design of a single metabolite profiling experiment with the x-axis representing the time scale. Branches of the tree are used to describe the plant’s environmental condition. Recorded environmental conditions are either given to describe the general experimental setup and to support cross experiment comparisons, or to indicate the specific stress type. A “salt stress experiment” is described using different salt concentrations. Clicking the nodes of the tree, quantitative environmental conditions (e.g. temperature, salt concentrations, humidity, etc.) describing the plant’s environment can be inspected in the right table. Unfortunately, due to the limitations of the current html based visualisation, the scaling of the tree's branches is not proportional to the real length of time. Green tagged observation points (OP) represent sampling time points. Results in the data analysis (see heat map or MapMan links in table on top) correspond to these observation points. Please note that observation point names (OP1, OP2, etc.) do not relate to each other. Instead, use the description of the observation points to identify potential candidates for cross experiment profile comparison.
service last updated 31/08/2021 © 2008-2014 Golm Metabolome Database - All rights reserved
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