ARC Data Publications Gaining Traction

Thu Dec 12 2024

One of the main objectives of DataPLANT is to foster a cultural shift toward data publications. The Annotated Research Contexts (ARCs) serve as containers for experimental data, computational analyses, and their annotations. It is a conceptual framework adhering to the RO-Crate specification. For fundamental plant researchers, data publications are becoming a positive indicator of career success. DataPLANT, in collaboration with the plant science research community, is dedicated to embedding this practice as a core element of the digital transformation in science.

Recently, the Fernie Lab at the Max Planck Institute of Molecular Plant Physiology (MPIMP) in P otsdam, a member of DataPLANT, published an ARC focusing on the characterization of a variegated tomato mutant named canalized-1. This research employed a multi-omics approach, incorporating transcriptomics, proteomics, and metabolomics. The canalized-1 mutant, previously described as a yield canalization mutant, has been linked to the AtSCO2 (SNOWY COTYLEDONS2) ortholog, a gene identified as a photosystem assembly factor in Arabidopsis thaliana.

The multi-omics analysis revealed distinct responses in white and green leaf sectors at various omics levels. Findings suggested that green leaf sectors establish functional photosystems despite the impaired protein encoded by the mutated gene. This compensation occurs via transcriptional overexpression of photosystem assembly genes. These results further validate the role of the mutated protein as a photosystem assembly factor. Additionally, the observed yield decanalization likely stems from variations in total photosynthetically active leaf area between plants.

The study highlights the potential of ARCs to advance plant science research. The original data publisher, formerly a DataPLANT data steward, now serves as a senior research officer (postdoc) in Christine Raines’ group and contributes to the RIPE consortium. This group is working to enhance the regeneration of ribulose bisphosphate (RuBP) and thereby improve photosynthetic efficiency.