Software supporting: RNA-Seq analysis of Brassicaceae species under different irradiances

doi: 10.4121/5b88cdf2-eb5f-4033-8ece-1f3f488a1f83.v1
The doi above is for this specific version of this dataset, which is currently the latest. Newer versions may be published in the future. For a link that will always point to the latest version, please use
doi: 10.4121/5b88cdf2-eb5f-4033-8ece-1f3f488a1f83
Datacite citation style:
Garassino, Francesco (2023): Software supporting: RNA-Seq analysis of Brassicaceae species under different irradiances. Version 1. 4TU.ResearchData. software.
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite
Wageningen University and Research logo
usage stats

This software package contains all scripts employed to analyze data from an RNA-Seq experiment conducted on Brassicaceae species grown under different irradiances. In this study, co-authors and I aimed to comprehend the genetic and physiological underpinnings of photosynthetic light-use efficiency (LUE) under high irradiance conditions, focusing on the plant species Hirschfeldia incana. We performed a comparison of the transcriptional signature associated to very high, "supernatural" irradiance in H. incana with three other Brassicaceae plants (Arabidopsis thaliana, Brassica rapa, and Brassica nigra), which previously demonstrated lower photosynthetic LUE. By utilizing a panproteome, we assessed gene expression patterns in response to high irradiance across the four species. Our findings reveal that all species actively regulate genes linked to photosynthesis. Analyzing genes associated with three key photosynthetic pathways, we observed a consistent pattern of reduced gene expression under high irradiance conditions. Notably, specific genes exhibited differential expression exclusively in H. incana, while in other instances, transcript abundance was consistently higher in H. incana regardless of light intensity. In conclusion, the study this software supports presents the first comparative transcriptome analysis of plant species grown entirely under prolonged high irradiance, rather than just briefly exposed to it. We demonstrate that, in contrast to other Brassicaceae species, H. incana subjected to intense irradiance displays enhanced gene expression related to photosynthesis through distinct mechanisms: canonical differential expression, inherent elevated expression of single-copy genes, and cumulative elevated expression via simultaneous expression of multiple gene copies. This research establishes a crucial groundwork for future endeavors aimed at comprehending elevated photosynthetic light-use efficiency and ultimately achieving highly effective photosynthesis in agricultural crops.

  • 2023-08-17 first online, published, posted
Snakemake pipeline, Python scripts, R scripts
Wageningen University & Research


To access the source code, use the following command:

git clone
files (1)