From 2f91cb057fd62016e33d934b26d8e5306c24def6 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus <brilhaus@nfdi4plants.org> Date: Wed, 5 Feb 2025 14:51:57 +0100 Subject: [PATCH] polish automated README and merge with mermaid --- README.md | 152 +++++++++++++++++++++++++++---------------------- arc-mermaid.md | 33 ----------- 2 files changed, 85 insertions(+), 100 deletions(-) delete mode 100644 arc-mermaid.md diff --git a/README.md b/README.md index 70f7be4..813056a 100644 --- a/README.md +++ b/README.md @@ -1,44 +1,83 @@ # Facultative CAM in Talinum - ## Data origin - 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> <!--- Start of automated section --> # Facultative CAM in Talinum triangulare + +## Table of Contents + +1. [Description](#description) +1. [Contacts](#contacts) +2. [Publication](#publication) +3. Studies + - [TalinumGenomeDraft](#study--talinumgenomedraft) + - [TalinumFacultativeCAM](#study--talinumfacultativecam) +4. Assays + - [MassHunter_targets](#assay--masshunter_targets) + - [Talinum_RNASeq_minimal](#assay--talinum_rnaseq_minimal) + - [GCqTOF_targets](#assay--gcqtof_targets) + ### 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. -<<Test ARC registry>> - ## Relationships between Assays and Studies - +## Relationships between Assays and Studies + ```mermaid --- title: Facultative-CAM-in-Talinum --- -graph TB -TalinumGenomeDraft_study["TalinumGenomeDraft"]; -TalinumFacultativeCAM_study["TalinumFacultativeCAM"]; -MassHunter_targets_assay["MassHunter_targets"]; -Talinum_RNASeq_minimal_assay["Talinum_RNASeq_minimal"]; -GCqTOF_targets_assay["GCqTOF_targets"]; -TalinumFacultativeCAM_study --> Talinum_RNASeq_minimal_assay; -TalinumFacultativeCAM_study --> GCqTOF_targets_assay ; -GCqTOF_targets_assay --> MassHunter_targets_assay -class TalinumGenomeDraft_study,TalinumFacultativeCAM_study study; -class MassHunter_targets_assay,Talinum_RNASeq_minimal_assay,GCqTOF_targets_assay assay; -classDef assay fill:#4FB3D9,stroke:#333,stroke-width:2px,color:#3A3A3A; -classDef study fill:#B4CE82,stroke:#333,stroke-width:2px,color:#3A3A3A; + +flowchart TD + Facultative-CAM-in-Talinum[Facultative-CAM-in-Talinum] + Facultative-CAM-in-Talinum-->STUDY_TalinumGenomeDraft + subgraph STUDY_TalinumGenomeDraft[Study:TalinumGenomeDraft] + TalinumGenomeDraft[TalinumGenomeDraft] + end + Facultative-CAM-in-Talinum-->STUDY_TalinumFacultativeCAM + subgraph STUDY_TalinumFacultativeCAM[Study:TalinumFacultativeCAM] + plant_material[plant_material] + end + subgraph ASSAY_MassHunter_targets[Assay:MassHunter_targets] + mh-quant-results[mh-quant-results] + mh-quant-report[mh-quant-report] + end + subgraph ASSAY_Talinum_RNASeq_minimal[Assay:Talinum_RNASeq_minimal] + rna_extraction[rna_extraction] + illumina[illumina] + end + subgraph ASSAY_GCqTOF_targets[Assay:GCqTOF_targets] + metabolite_extraction[metabolite_extraction] + gas_chromatography[gas_chromatography] + mass_spec[mass_spec] + end + plant_material-->|6|rna_extraction + plant_material-->|6|metabolite_extraction + mh-quant-results-->|1|mh-quant-report + rna_extraction-->|6|illumina + metabolite_extraction-->|6|gas_chromatography + gas_chromatography-->|20|mass_spec + mass_spec-->|20|mh-quant-results + +classDef investigationStyle fill:#6c7885,color:#2d3e50,font-weight:bold; +classDef studyStyle fill:#62d4c1,color:#2d3e50,font-weight:bold; +classDef assayStyle fill:#ffd34d,color:#2d3e50,font-weight:bold; +classDef processStyle fill:#D46275,color:#2d3e50,font-weight:; +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 | Assay identifiers | MassHunter_targets , Talinum_RNASeq_minimal , GCqTOF_targets | | Assay Count | 3 | -## Table of Contents - -1. [Contacts](#contacts) - - 2. [Publication](#publication) - - 3. Studies +## Contacts - - [TalinumGenomeDraft](#study--talinumgenomedraft) - - [TalinumFacultativeCAM](#study--talinumfacultativecam) - 4. Assays - - - [MassHunter_targets](#assay--masshunter_targets) - - [Talinum_RNASeq_minimal](#assay--talinum_rnaseq_minimal) - - [GCqTOF_targets](#assay--gcqtof_targets) - 5. [References](#references) - -## Contacts - | Names | Email | Address | Affiliation | ORCID | | ----- | ----- | ------- | ----------- | ----- | -| Dominik Brilhaus | brilhaus@hhu.de | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | http://orcid.org/0000-0001-9021-3197 | - | 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 | +| Dominik Brilhaus | <brilhaus@hhu.de> | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0001-9021-3197> | + | 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 | Data File Count | 0 | | Associated assays | Talinum_RNASeq_minimal , GCqTOF_targets | | Biological replicates | 0 | + ### Annotation headers **Characteristics**: [organism](https://bioregistry.io/OBI:0100026),[organism part](https://bioregistry.io/EFO:0000635),[plant age](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000033) @@ -119,12 +143,10 @@ _Figure 1:This flowchart highlights the relationship between assays (highlighted **Factors**: [watering exposure](https://bioregistry.io/PECO:0007383),[Timepoint](https://bioregistry.io/NCIT:C68568),`timepoint-ZT`,`Photosynthesis mode` -## Assay : _MassHunter_targets_ -### 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 : *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 | Sample Count | 6 | | Data File Count | 6 | | Associated studies | TalinumFacultativeCAM | + ### Annotation headers **Parameters**: [biosource amount](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000013),[extraction method](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000054),[extraction buffer](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000050),[extraction buffer volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000051),[RNA quality check](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000062),[library strategy](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000035),[library selection](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000036),[library layout](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000015),[library preparation kit](http://purl.obolibrary.org/obo/GENEPIO_0000085),[library preparation kit version](http://purl.obolibrary.org/obo/GENEPIO_0000149),[adapter sequence](http://purl.obolibrary.org/obo/GENEPIO_0000083),[next generation sequencing instrument model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000040),[base-calling software](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000017),[base-calling software version](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000018),[Raw data file format](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000021) -## Assay : _GCqTOF_targets_ -### 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 : *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 | Sample Count | 20 | | Data File Count | 20 | | Associated studies | TalinumFacultativeCAM | + ### Annotation headers **Parameters**: [Bio entity](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000012),[Biosource amount](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000013),[Biosource material state](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010009),[Extraction buffer](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000050),[Extraction buffer volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000051),[Internal standard](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010012),[Sample volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010013),[MS sample post-extraction](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000043),[MS sample resuspension](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000044),[MS derivatization](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000052),[MS sample type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000045),[Chromatography instrument model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000046),[Chromatography autosampler model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000047),[Chromatography column type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000053),[Chromatography column model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000048),[mobile phase](http://purl.obolibrary.org/obo/CHMO_0000995),[Chromatography injection volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010014),[Chromatography injection mode](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010015),[Chromatography gradient](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000081),[scan polarity](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000465),[scan window lower limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000501),[scan window upper limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000500),[scan rate](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000015),[instrument model](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000031),[ionization type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000008),[mass analyzer type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000443),[detector type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000026) -## References - _add your references here_ - <!--- End of automated section --> \ No newline at end of file diff --git a/arc-mermaid.md b/arc-mermaid.md deleted file mode 100644 index 85b9079..0000000 --- a/arc-mermaid.md +++ /dev/null @@ -1,33 +0,0 @@ -```mermaid -flowchart LR - Facultative-CAM-in-Talinum[Facultative-CAM-in-Talinum] - Facultative-CAM-in-Talinum-->Study:TalinumGenomeDraft - subgraph Study:TalinumGenomeDraft - TalinumGenomeDraft[TalinumGenomeDraft] - end - Facultative-CAM-in-Talinum-->Study:TalinumFacultativeCAM - subgraph Study:TalinumFacultativeCAM - plant_material[plant_material] - end - subgraph Assay:MassHunter_targets - mh-quant-results[mh-quant-results] - mh-quant-report[mh-quant-report] - end - subgraph Assay:Talinum_RNASeq_minimal - rna_extraction[rna_extraction] - illumina[illumina] - end - subgraph Assay:GCqTOF_targets - metabolite_extraction[metabolite_extraction] - gas_chromatography[gas_chromatography] - mass_spec[mass_spec] - end - plant_material-->|6|rna_extraction - plant_material-->|6|metabolite_extraction - mh-quant-results-->|1|mh-quant-report - rna_extraction-->|6|illumina - metabolite_extraction-->|6|gas_chromatography - gas_chromatography-->|20|mass_spec - mass_spec-->|20|mh-quant-results - -``` -- GitLab