From aa7201d0c9ed43539ea7ec6835221ab6e3f2d4fb Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus <brilhaus@nfdi4plants.org> Date: Wed, 5 Mar 2025 12:58:33 +0100 Subject: [PATCH] add auto readme and mermaid --- README.md | 242 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 242 insertions(+) diff --git a/README.md b/README.md index 767e4ab..3733f02 100644 --- a/README.md +++ b/README.md @@ -44,3 +44,245 @@ Results of the genome sequencing and transcriptome analysis. [Supplemental Material](https://git.nfdi4plants.org/usadellab/ribes_nigrum_genome/-/blob/main/studies/Supplemental_Tables.xlsx?ref_type=heads) + + +<!--- Start of automated section --> + +# A full genome assembly reveals drought stress effects on gene expression and metabolite profiles in blackcurrant (Ribes nigrum L.) + +### Description +Blackcurrant (Ribes nigrum L.) is valued for its nutrient-rich berries, yet drought stress during fruiting can hinder growth and reduce yields. We present the first high-quality chromosome-scale genome assembly for blackcurrant, analyzing the transcriptomic response of leaves and roots to drought. This analysis revealed key drought-responsive genes and metabolic shifts, including increased proline and decreased organic acids. Our findings offer a genomic foundation to support breeding of drought-resistant blackcurrant varieties. + +## Table of Contents + + 1. Studies + + - [Ribes_nigrum_drought_exp1](#study--ribes_nigrum_drought_exp1) + - [Ribes_nigrum_drought_exp2](#study--ribes_nigrum_drought_exp2) + - [Ribes_nigrum_genome](#study--ribes_nigrum_genome) + + 2. Assays + + - [RNASeq_drought](#assay--rnaseq_drought) + - [Ribes_nigrum_genome_sequencing](#assay--ribes_nigrum_genome_sequencing) + - [Metabolite_measurement](#assay--metabolite_measurement) + - [qRT-PCR](#assay--qrt-pcr) + +## Relationships between Assays and Studies + +```mermaid +--- +title: Ribes_nigrum_genome +--- +flowchart TD + classDef investigationStyle fill:#6c7885,color:#2d3e50,fontWeight:bold; + classDef studyStyle fill:#62d4c1,color:#2d3e50,fontWeight:bold; + classDef assayStyle fill:#ffd34d,color:#2d3e50,fontWeight:bold; + classDef processStyle fill:#D46275,color:#2d3e50; + id_0["A full genome assembly reveals drought stress effects on gene expression and metabolite profiles in blackcurrant (Ribes nigrum L.)"] + class id_0 investigationStyle; + id_0-->STUDY_id_1 + class STUDY_id_1 studyStyle; + subgraph STUDY_id_1[Study: Ribes nigrum Drought Experiment 1] + id_2[Plant growth] + class id_2 processStyle; + end + id_0-->STUDY_id_3 + class STUDY_id_3 studyStyle; + subgraph STUDY_id_3[Study: Ribes nigrum Drought Experiment 2] + id_4[plant_growth] + class id_4 processStyle; + end + id_0-->STUDY_id_0 + class STUDY_id_0 studyStyle; + subgraph STUDY_id_0[Study: Ribes nigrum Genome] + id_2[Plant growth] + class id_2 processStyle; + end + subgraph ASSAY_id_5[Assay: RNASeq_drought] + id_6[RNASeq] + class id_6 processStyle; + end + class ASSAY_id_5 assayStyle; + subgraph ASSAY_id_7[Assay: Ribes_nigrum_genome_sequencing] + id_8[DNA_library_and_sequencing] + class id_8 processStyle; + end + class ASSAY_id_7 assayStyle; + subgraph ASSAY_id_9[Assay: Metabolite_measurement] + id_10[metabolite_analysis] + class id_10 processStyle; + end + class ASSAY_id_9 assayStyle; + subgraph ASSAY_id_11[Assay: qRT-PCR] + id_12[qRTPCR] + class id_12 processStyle; + end + class ASSAY_id_11 assayStyle; + id_2-->|12|id_6 + id_2-->|12|id_10 + id_2-->|12|id_12 + id_4-->|6|id_6 + id_4-->|6|id_10 + id_4-->|6|id_12 + id_13-->|1|id_8 +``` + +### Additional details +| Meta Data | Description | +| --------- | ----------- | +| Submission Date | tba | +| Public Release Date | tba | +| Study identifiers | Ribes_nigrum_drought_exp1 , Ribes_nigrum_drought_exp2 , Ribes_nigrum_genome | +| Study Count | 3 | +| Assay identifiers | RNASeq_drought , Ribes_nigrum_genome_sequencing , Metabolite_measurement , qRT-PCR | +| Assay Count | 4 | + +## Contacts + +| Names | Email | Address | Affiliation | ORCID | +| ----- | ----- | ------- | ----------- | ----- | +| Freya Maria Rosemarie Ziegler | f.ziegler@fz-juelich.de | Wilhelm-Johnen-Straße, D-52425 Jülich, Germany; Universitätsstr. 1, D-40225 Düsseldorf, Germany; Universitätsstr. 1, D-40225 Düsseldorf, Germany | CEPLAS, Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), Forschungszentrum Jülich; Faculty of Mathematics and Natural Sciences, CEPLAS, Institute for Biological Data Science, Heinrich Heine University Düsseldorf; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf | | + | Vivien Rosenthal | viros101@uni-duesseldorf.de | Universitätsstr. 1, D-40225 Düsseldorf, Germany; Universitätsstr. 1, D-40225 Düsseldorf, Germany | Faculty of Mathematics and Natural Sciences, CEPLAS, Institute for Biological Data Science, Heinrich Heine University Düsseldorf; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf | | + | José G. Vallarino | vallarino@uma.es | 9010 Málaga, Spain | Departamento de BiologÃa Molecular y BioquÃmica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones CientÃficas | 0000-0002-0374-8706 | + | Franziska Genzel | f.genzel@fz-juelich.de | Wilhelm-Johnen-Straße, D-52425 Jülich, Germany | CEPLAS, Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), Forschungszentrum Jülich | 0000-0003-2217-8136 | + | Sarah Spettmann | s.spettmann@fz-juelich.de | Wilhelm-Johnen-Straße, D-52425 Jülich, Germany | CEPLAS, Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), Forschungszentrum Jülich | | + | Åukasz Seliga | lukasz.seliga@inhort.pl | Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland | Department of Plant Crop breeding, INHORT, National Institute of Horticultural Research | 0000-0002-1687-5499 | + | Sylwia Keller-PrzybyÅ‚kowicz | sylwia.keller@inhort.pl | Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland | Department of Plant Crop breeding, INHORT, National Institute of Horticultural Research | 0000-0002-3473-9706 | + | Lucas Munnes | lucas.munnes@hhu.de | Universitätsstr. 1, D-40225 Düsseldorf, Germany | Faculty of Mathematics and Natural Sciences, CEPLAS, Institute for Biological Data Science, Heinrich Heine University Düsseldorf | | + | Anita Sønsteby | anita.sonsteby@nibio.no | Pb. 115, NO-1431 Ã…s, Norway | NIBIO, Norwegian Institute of Bioeconomy Research, Division of Food Production and Society Horticulture | 0000-0002-2705-9091 | + | Sonia Osorio | sosorio@uma.es | 9010 Málaga, Spain | Departamento de BiologÃa Molecular y BioquÃmica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones CientÃficas | 0000-0002-0159-6091 | + | Björn Usadel | b.usadel@fz-juelich.de | Wilhelm-Johnen-Straße, D-52425 Jülich, Germany; Universitätsstr. 1, D-40225 Düsseldorf, Germany; Universitätsstr. 1, D-40225 Düsseldorf, Germany | CEPLAS, Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), Forschungszentrum Jülich; Faculty of Mathematics and Natural Sciences, CEPLAS, Institute for Biological Data, Heinrich Heine University Düsseldorf; ScienceCluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf; | 0000-0003-0921-8041 | + +## Study: _Ribes_nigrum_drought_exp1_ +### Description +To investigate the physiological and molecular response of blackcurrant leaves and roots to drought stress in mature plants, irrigation was withheld for a period of 4 days. This experimental setup aimed to simulate moderate drought conditions and enable the assessment of changes in plant behavior, including water-use efficiency, photosynthetic activity, and stress-related gene expression. By examining both aboveground (leaves) and belowground (roots) tissues, the study provides a comprehensive understanding of the plant's adaptive mechanisms to water scarcity. + +### Additional details +| Meta Data | Description | +| --------- | ----------- | +| Table Count | 1 | +| Table Names | Plant growth | +| Sample Count | 12 | +| Data File Count | 0 | +| Associated assays | RNASeq_drought , Metabolite_measurement , qRT-PCR | +| Biological replicates | 0 | + +### Annotation headers + +**Characteristics**: [organism](https://bioregistry.io/OBI:0100026),[plant structure development stage](https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0009012),[geographic area](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000074),[plant structure](https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0009011) + +**Parameters**: [isolation and growth condition](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000030),[Container volume](http://purl.obolibrary.org/obo/MIAPPE_0118),[plant growth medium exposure](https://bioregistry.io/PECO:0007147) + +**Factors**: [watering exposure](https://bioregistry.io/PECO:0007383),[Experiment End Date](https://bioregistry.io/NCIT:C90382) + +## Study: _Ribes_nigrum_drought_exp2_ +### Description +To validate the response of blackcurrant plants to drought stress, irrigation was withheld for a period of 9 days. Drought stressed plants were compared to plants with continuous irrigation. Leaves were sampled for expression and metabolite analysis. + +### Additional details +| Meta Data | Description | +| --------- | ----------- | +| Table Count | 1 | +| Table Names | plant_growth | +| Sample Count | 6 | +| Data File Count | 0 | +| Associated assays | RNASeq_drought , Metabolite_measurement , qRT-PCR | +| Biological replicates | 0 | + +### Annotation headers + +**Characteristics**: [organism](https://bioregistry.io/OBI:0100026),[plant structure development stage](https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0009012),[geographic area](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000074),[plant structure](https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0009011) + +**Parameters**: [Container volume](http://purl.obolibrary.org/obo/MIAPPE_0118),[watering exposure](https://bioregistry.io/PECO:0007383) + +**Factors**: [isolation and growth condition](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000030) + +## Study: _Ribes_nigrum_genome_ + +### Description +The German cultivar Rosenthals Langtraubige was chosen for genomic analysis due to its vigorous, spreading growth habit and medium-sized, early-maturing berries with high vitamin C content. For the sequencing, we employed a combination of PacBio HiFi and Oxford Nanopore Technologies (ONT), integrating the Pore-C method for advanced chromosome conformation capture. + +### Additional details +| Meta Data | Description | +| --------- | ----------- | +| Table Count | 1 | +| Table Names | Plant growth | +| Sample Count | 1 | +| Data File Count | 0 | +| Associated assays | Ribes_nigrum_genome_sequencing | +| Biological replicates | 0 | +### Annotation headers + +**Characteristics**: [organism](https://bioregistry.io/OBI:0100026),[plant structure development stage](https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0009012),[geographic area](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000074),[plant structure](https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0009011) + +## Assay: _RNASeq_drought_ + +### Additional details + +| Meta Data | Description | +| --------- | ----------- | +| Measurement Type | Gene Expression Analysis | +| Technology Type | RNA-Seq | +| Table Count | 1 | +| Table Names | RNASeq | +| Sample Count | 18 | +| Data File Count | 18 | +| Associated studies | Ribes_nigrum_drought_exp1 , Ribes_nigrum_drought_exp2 | + +### Annotation headers + +**Characteristics**: [Sequencing Library Source Indicator](https://bioregistry.io/NCIT:C175895) + +**Parameters**: [total RNA extraction](https://bioregistry.io/OBI:0000855),[Library selection](http://purl.obolibrary.org/obo/GENEPIO_0001940),[library strategy](http://purl.obolibrary.org/obo/GENEPIO_0001973) + +## Assay: _Ribes_nigrum_genome_sequencing_ +### Additional details +| Meta Data | Description | +| --------- | ----------- | +| Measurement Type | Whole Genome Sequencing | +| Table Count | 1 | +| Table Names | DNA_library_and_sequencing | +| Sample Count | 3 | +| Data File Count | 3 | +| Associated studies | Ribes_nigrum_genome | + +### Annotation headers + +**Characteristics**: [Sequencing Library Source Indicator](https://bioregistry.io/NCIT:C175895) + +**Parameters**: [Library selection](http://purl.obolibrary.org/obo/GENEPIO_0001940),[library strategy](http://purl.obolibrary.org/obo/GENEPIO_0001973),[library layout](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000015) + +## Assay: _Metabolite_measurement_ + +### Additional details +| Meta Data | Description | +| --------- | ----------- | +| Measurement Type | metabolite measurement | +| Technology Type | Gas Chromatography Mass Spectrometry | +| Table Count | 1 | +| Table Names | metabolite_analysis | +| Sample Count | 18 | +| Data File Count | 18 | +| Associated studies | Ribes_nigrum_drought_exp1 , Ribes_nigrum_drought_exp2 | + +### Annotation headers + +**Parameters**: [technology type](http://purl.obolibrary.org/obo/ARC_00000068),[data transformation](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000452) + +## Assay: _qRT-PCR_ +### Additional details +| Meta Data | Description | +| --------- | ----------- | +| Measurement Type | gene expression measurement | +| Technology Type | Real Time PCR | +| Table Count | 1 | +| Table Names | qRTPCR | +| Sample Count | 18 | +| Data File Count | 18 | +| Associated studies | Ribes_nigrum_drought_exp1 , Ribes_nigrum_drought_exp2 | +### Annotation headers + +**Parameters**: [technical replicate](https://bioregistry.io/EFO:0002090) + +<!--- End of automated section --> -- GitLab