diff --git a/README.md b/README.md index 0c634d06a0825282e5069a27e5c6ece341e8c95b..637b19497f8c13da5f72c2760a1df5513788927b 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,10 @@ -# 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. + + [Supplemental Material](https://git.nfdi4plants.org/usadellab/ribes_nigrum_genome/-/blob/main/studies/Supplemental_Tables.xlsx?ref_type=heads) diff --git a/assays/RNASeq_drought/isa.assay.xlsx b/assays/RNASeq_drought/isa.assay.xlsx index 5721324415897913cc8cd651223d25ccac20a774..34091770017d4c200ac3b725712e7794b15870ac 100644 Binary files a/assays/RNASeq_drought/isa.assay.xlsx and b/assays/RNASeq_drought/isa.assay.xlsx differ diff --git a/studies/Ribes_nigrum_genome/README.md b/studies/Ribes_nigrum_genome/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..7cc16d7c0a21b9e2a879f99b1acdea17a667da2d 100644 --- a/studies/Ribes_nigrum_genome/README.md +++ b/studies/Ribes_nigrum_genome/README.md @@ -0,0 +1,4 @@ +# *Ribes nigrum* sequencing experiment + + +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. \ No newline at end of file diff --git a/studies/Ribes_nigrum_genome/resources/RibesNigrum_Greenhouse.jpeg b/studies/Ribes_nigrum_genome/resources/RibesNigrum_Greenhouse.jpeg new file mode 100644 index 0000000000000000000000000000000000000000..4675a5cdc85c8c928b5e5e8610b62db03f40b2e4 Binary files /dev/null and b/studies/Ribes_nigrum_genome/resources/RibesNigrum_Greenhouse.jpeg differ diff --git a/studies/Ribes_nigrum_transcriptome/README.md b/studies/Ribes_nigrum_transcriptome/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..c1e6abc633f5b3879c60594abb49a997f73ec42d 100644 --- a/studies/Ribes_nigrum_transcriptome/README.md +++ b/studies/Ribes_nigrum_transcriptome/README.md @@ -0,0 +1,10 @@ + +# Drought stress experiment + +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. + + + + + +Figure from [Ziegler et al. 2024](https://doi.org/10.1093/hr/uhae313) \ No newline at end of file diff --git a/studies/Ribes_nigrum_transcriptome/protocols/greenhouse_drought_experiment.png b/studies/Ribes_nigrum_transcriptome/protocols/greenhouse_drought_experiment.png new file mode 100644 index 0000000000000000000000000000000000000000..4fa29e6697e3ec694c0d6119d2fbecc8663df79e Binary files /dev/null and b/studies/Ribes_nigrum_transcriptome/protocols/greenhouse_drought_experiment.png differ