- see [isa.investigation.xlsx](./isa.investigation.xlsx) for details
- Adapted from
> Brilhaus, D., Bräutigam, A., Mettler-Altmann, T., Winter, K., and Weber, A.P.M. (2016). Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in *Talinum triangulare*. Plant Physiology 170: 102–122. https://doi.org/10.1104/pp.15.01076
-[studies/TalinumGenomeDraft](./studies/TalinumGenomeDraft) originates from https://git.nfdi4plants.org/hhu-plant-biochemistry/talinum-fruticosum-genome
> Brilhaus, D., Bräutigam, A., Mettler-Altmann, T., Winter, K., and Weber, A.P.M. (2016). Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in *Talinum triangulare*. Plant Physiology 170: 102–122. <https://doi.org/10.1104/pp.15.01076>
-[studies/TalinumGenomeDraft](./studies/TalinumGenomeDraft) originates from <https://git.nfdi4plants.org/hhu-plant-biochemistry/talinum-fruticosum-genome>
Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
class Facultative-CAM-in-Talinum investigationStyle;
class STUDY_TalinumGenomeDraft,STUDY_TalinumFacultativeCAM studyStyle;
class ASSAY_MassHunter_targets,ASSAY_Talinum_RNASeq_minimal,ASSAY_GCqTOF_targets assayStyle;
class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_extraction,illumina,metabolite_extraction,gas_chromatography,mass_spec processStyle;
```
_Figure 1:This flowchart highlights the relationship between assays (highlighted in blue) and studies (highlighted in green)_
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Submission Date | July 07, 2015 |
...
...
@@ -48,34 +87,17 @@ _Figure 1:This flowchart highlights the relationship between assays (highlighted
| Andrea Bräutigam | andrea.brauetigam@hhu.de | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | http://orcid.org/0000-0002-5309-0527 |
| Tabea Mettler-Altmann | tabea.mettler@hhu.de | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | http://orcid.org/0000-0002-9161-4889 |
| Klaus Winter | winterk@si.edu | Balboa, Ancón, Republic of Panama | Smithsonian Tropical Research Institute, Panama | |
| Andreas P M Weber | aweber@hhu.de | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | http://orcid.org/0000-0003-0970-4672 |
| Andrea Bräutigam | <andrea.brauetigam@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0002-5309-0527> |
| Tabea Mettler-Altmann | <tabea.mettler@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0002-9161-4889> |
| Klaus Winter | <winterk@si.edu> | Balboa, Ancón, Republic of Panama | Smithsonian Tropical Research Institute, Panama | |
| Andreas P M Weber | <aweber@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0003-0970-4672> |
## Publication
## Publication
| Meta Data | Description |
| ----------- | ----------- |
...
...
@@ -85,10 +107,10 @@ _Figure 1:This flowchart highlights the relationship between assays (highlighted
| DOI | 10.1104/pp.15.01076 |
| Current status | Published |
## Study : _TalinumGenomeDraft_
### Description
tba
## Study : *TalinumGenomeDraft*
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Table Count | 1 |
...
...
@@ -97,12 +119,13 @@ _Figure 1:This flowchart highlights the relationship between assays (highlighted
| Data File Count | 1 |
| Associated assays | |
| Biological replicates | 0 |
### Annotation headers
## Study : _TalinumFacultativeCAM_
### Description
tba
## Study : *TalinumFacultativeCAM*
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Table Count | 1 |
...
...
@@ -111,6 +134,7 @@ _Figure 1:This flowchart highlights the relationship between assays (highlighted
Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
## Assay : *MassHunter_targets*
<<Test ARC registry>>
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Table Count | 2 |
...
...
@@ -132,14 +154,13 @@ Drought tolerance is a key factor for agriculture in the 21st century as it is a
| Sample Count | 20 |
| Data File Count | 21 |
| Associated studies | |
### Annotation headers
## Assay : _Talinum_RNASeq_minimal_
### Description
Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
## Assay : *Talinum_RNASeq_minimal*
<<Test ARC registry>>
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Measurement Type | mRNA Sequencing |
...
...
@@ -149,16 +170,15 @@ Drought tolerance is a key factor for agriculture in the 21st century as it is a
Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
## Assay : *GCqTOF_targets*
<<Test ARC registry>>
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Measurement Type | GCqTOF targeted |
...
...
@@ -167,11 +187,9 @@ Drought tolerance is a key factor for agriculture in the 21st century as it is a
