Plant Reactome Release Summary - Version 24 - April 2025

The April 2025 public release (Version 24) of the Plant Reactome pathway knowledgebase hosts pathways for 139 species representing model plants, crops, and species of evolutionary importance. It is an open-source and freely accessible resource, built upon the Neo4j graph database management system to facilitate a seamless integration of heterogeneous data (i.e., genes, proteins, metabolites, gene-regulatory interactions, protein-protein interactions, enzymatic reactions, gene expression, pathways, gene networks, etc.) by leveraging the Gene Ontologies (GO) and Plant Ontologies (PO). We use rice (Oryza sativa) as a model for the biocuration of pathways based on empirical evidence from published scientific literature and information extracted from the re-analysis of genomic (e.g., motif binding/DAP-seq/ChIP-seq) and gene-expression data. We utilized the reference rice pathways for the generation of gene-orthology-based automated pathway projection on an additional 138 species. Plant Reactome provides a valuable framework for understanding how a gene, a group of connected genes, or genotypic differences culminate into a phenotype. It also allows users to upload their OMICs data for analysis and visualization in the context of a system-level pathway network for discovery of new knowledge/candidate genes and pathways or for generating data-driven hypotheses for advancing basic and translational research. We implement and encourage the Findable, Accessible, Interoperable and Re-usable (FAIR) policy.

Full release summary  is available at Link . Here we provide highlights of the Plant Reactome  April 2025 release:

1. Updates on Curation of reference rice pathways

The focus of April 2025 release has been on curation of the pathways related to response to abiotic stress/stimuli and how they shape plant architecture and development. We have added 9 new pathways nested inside 3 new categories (container pathways), including ‘Flowering under drought stress’, ‘Root Gravitropism’, and ‘Shoot Gravitropism’. 1 new pathway ‘TF network involved in salinity response’ was nested under ‘Response to salinity’. In addition, we updated 5 previous pathways. This release includes addition of 114 new scientific papers (total 1026 curated references to date). Overall, we have 351 manually curated rice reference pathways (consisting of 2098 reaction, 2233 gene products and 1,320 small molecules) and their gene-orthology-based projections to 138 species totaling >38,000 pathways, >118,000 reactions, and >263,000 proteins and >1320 small molecules. Below is the list of new and updated pathways.

Key:
Black = existing pathway
Red = new container pathway
Green = new pathway
Blue = updated pathway
Pathway Browser links to Oryza sativa by default

Growth and Developmental Processes
    Reproductive structure development
        Inflorescence development
            Long day regulated expression of florigens (View)
            Short day regulated expression of florigens (View)
            Transition from vegetative to reproductive shoot apical meristem (View)
Responses to stimuli: abiotic stimuli and stresses
    Flowering under drought stress (View)
        Severe drought (View)
        Mild drought (View)
            Drought escape (DE) via ABA-dependent pathway (View)
            Drought escape (DE) via ABA-independent pathway (View)
    Gravitropism under notmal or artificial gravity environments
        Root gravitropism (View)
            Gravity sensing and statolith sedimentation (View)
            Root angle formation: elongation and curvature response (View)
            Starch biosynthesis (View)
        Shoot gravitropism: development, growth, and architecture of shoot in response to gravity (View)
            Gravity sensing and statolith sedimentation (View)
            Strigolactone-mediated axillary bud dormancy and suppression of tillering (View)
            Shoot (tiller) formation and regulation of tiller angle (View)
            Strigolactone signaling (View)
    Response to salinity
        TF network involved in salinity response (View)

2. New added species

In the Plant Reactome version 24 (April 2025), gene homology-based projections were added for the following 9 new species (an increase of ~10,000 new plant pathways)

1. Aegilops Umbellulata (umbel goatgrass) (taxon:4491)
2. Arachis Hypogaea (peanut) (taxon:3818)
3. Avena Sativa Ot3098 (oat) (taxon:4498)
4. Fraxinus Excelsior (European ash tree) (taxon:38873)
5. Glycine Soja (wild soybean) (taxon:3848)
6. Lathyrus Sativus (Indian pea) (taxon:3860)
7. Triticum Spelta (spelt) (taxon:2529948)
8. Triticum Timopheevii (Zanduri wheat) (taxon:58932)
9. Vicia Faba (fava bean) (taxon:1706215)

3. Training: 

We engaged and trained 9 undergraduate students (1 in 2025, 3 in 2024 and 5 in 2023) in review of scientific literature, transcriptome data analysis, and biocuration. 

4. Analytical tools

Plant Reactome is cross-referenced to many bioinformatics databases. These include project databases like Gramene, Ensembl-Plant Gene Expression Atlas, and ChEBI small molecule databases. Recently, we have embedded a DiagramJS pathway widget, a dynamic, interactive pathway viewer, into the GLDS website (Space Biology Data Visualization Apps: https://genelab.nasa.gov/external-vis-apps) to facilitate space biology researchers in navigation of the Plant Reactome database, and OMICs data/pathways enrichment analysis.

Currently, Plant Reactome supports researchers with the following analytical tools:
- Search for gene/protein, metabolites, pathways
- Upload and analyze gene-expression data on plant pathways
- Upload and analyze gene-gene interaction data on plant pathways
- Compare reference rice pathways with pathways from any of 138 projected species hosted by Plant Reactome.