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Commit 507a935e authored by Hannah Dörpholz's avatar Hannah Dörpholz
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        ......@@ -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 Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas | 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 | |
        | Łukasz 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-Przybyłkowicz | 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 Ås, 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 Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas | 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 -->
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