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README.md

-#  Drought stress effects on gene expression and metabolite profiles in blackcurrant (Ribes nigrum L.)
+#  Drought stress effects on gene expression and metabolite profiles in blackcurrant (*Ribes nigrum* L.)
 
 Ziegler et al. 2024 Hort Res. https://doi.org/10.1093/hr/uhae313 
 
-The blackcurrant (Ribes nigrum L., family Grossulariaceae) is a perennial shrub valued for its antioxidant-rich berries, widely used in the food and beverage industry. However, prolonged drought during the fruiting season leads to drought stress, inhibiting growth and reducing yields. To explore the underlying molecular mechanisms, we present the first high-quality chromosome-scale genome assembly for blackcurrant (cv. Rosenthals Langtraubige), the first in the Grossulariaceae family. Using this genomic reference, we analyzed the transcriptomic response of blackcurrant leaves and roots to drought stress, identifying key differentially expressed genes and significant changes in primary metabolites, such as increased proline and depleted organic acids under stress. This data can aid in developing drought-resistant blackcurrant cultivars.
+The blackcurrant (*Ribes nigrum* L., family Grossulariaceae) is a perennial shrub valued for its antioxidant-rich berries, widely used in the food and beverage industry. However, prolonged drought during the fruiting season leads to drought stress, inhibiting growth and reducing yields. To explore the underlying molecular mechanisms, we present the first high-quality chromosome-scale genome assembly for blackcurrant (cv. Rosenthals Langtraubige), the first in the Grossulariaceae family. Using this genomic reference, we analyzed the transcriptomic response of blackcurrant leaves and roots to drought stress, identifying key differentially expressed genes and significant changes in primary metabolites, such as increased proline and depleted organic acids under stress. This data can aid in developing drought-resistant blackcurrant cultivars.
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+![](./studies/Ribes_nigrum_genome/resources/RibesNigrum_Greenhouse.jpeg)
 
 [Supplemental Material](https://git.nfdi4plants.org/usadellab/ribes_nigrum_genome/-/blob/main/studies/Supplemental_Tables.xlsx?ref_type=heads)
 

studies/Ribes_nigrum_genome/README.md

+# *Ribes nigrum* sequencing experiment
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+To generate a blackcurrant genome assembly, DNA of the cultivar *R. nigrum* Rosenthals Langtraubige was used. DNA was extracted from young leaves of a single adult plant. Sequencing was performed with Oxford Nanopore Technologies, PacBio HiFi and Illumina.
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studies/Ribes_nigrum_transcriptome/README.md

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+# Drought stress experiment
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+A greenhouse experiment was performed to investigate the influence of drought stress on the gene expression of *R. nigrum* cv Rosenthals Langtraubige. Stressed plants that were not watered for 4 days were compared to control plants with continuous irrigation. Both leaves and roots were sampled for RNA extraction.
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+![](./protocols/greenhouse_drought_experiment.png)
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+Figure from [Ziegler et al. 2024](https://doi.org/10.1093/hr/uhae313)
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