Recent Publications:

1. Murray S.C., A. Verhoef, A. Adak, D. Sen, R. Salzman, P. Jaiswal, and S. Naithani (2025). Detecting novel plant pathogen threats to food system security by integrating the Plant Reactome and remote sensing. Curr Opin Plant Biol. 83: 102684, doi:10.1016/j.pbi.2024.102684.
2. Gupta P., J. Elser, E. Hooks, P. D’Eustachio, P. Jaiswal and S. Naithani (2024). Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis. Nucleic Acids Res., 52 (D1): D1538-D1547, doi:10.1093/nar/gkad1052.
3. Naithani S., B. Mohanty, J. Elser, P. D’Eustachio, and P. Jaiswal (2023). Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa). Plants 12: 2146, doi:10.3390/plants12112146.
4. Andrew D Yates, James Allen, Ridwan M Amode, Andrey G Azov, Matthieu Barba, Andrés Becerra, Jyothish Bhai, Lahcen I Campbell, Manuel Carbajo Martinez, Marc Chakiachvili, Kapeel Chougule, Mikkel Christensen, Bruno Contreras-Moreira, Alayne Cuzick, Luca Da Rin Fioretto, Paul Davis, Nishadi H De Silva, Stavros Diamantakis, Sarah Dyer, Justin Elser, Carla V Filippi, Astrid Gall, Dionysios Grigoriadis, Cristina Guijarro-Clarke, Parul Gupta, Kim E Hammond-Kosack, Kevin L Howe, Pankaj Jaiswal, Vinay Kaikala, Vivek Kumar, Sunita Kumari, Nick Langridge, Tuan Le, Manuel Luypaert, Gareth L Maslen, Thomas Maurel, Benjamin Moore, Matthieu Muffato, Aleena Mushtaq, Guy Naamati, Sushma Naithani, Andrew Olson, Anne Parker, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Mark Quinton-Tulloch, Faye Rodgers, Marc Rosello, Magali Ruffier, James Seager, Vasily Sitnik, Michal Szpak, John Tate, Marcela K Tello-Ruiz, Stephen J Trevanion, Martin Urban, Doreen Ware, Sharon Wei, Gary Williams, Andrea Winterbottom, Magdalena Zarowiecki, Robert D Finn, Paul Flicek, Ensembl Genomes 2022: an expanding genome resource for non-vertebrates, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D996–D1003, https://doi.org/10.1093/nar/gkab1007
5. Tello-Ruiz M.K., Jaiswal P., Ware D. (2022) Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. In: Edwards D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2067-0_5
6. Gupta P., S. Naithani, J. Preece, S. Kim, P. D'Eustachio, J. Elser, E. Bolton, and P. Jaiswal (2022) Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. In: Edwards D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2067-0_27

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.

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)

New added species

This release adds 9 new species. Plant Reactome now hosts pathway projections for 139 plant species. The gene homology-based projections were added for the following new species:

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

In addition, the genes and orthology data was updated for Salvia hispanica (chia)

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.

We have extended orthology-based pathway projections for the additional 9 species from Ensembl. Plant Reactome now hosts pathway projections for 139 species ranging from unicellular autotrophs to higher plants

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*data from sequenced transcriptomes
^ projections currently exclude cell-cycle pathways and annotations
Planteome Inparanoid data was kindly provided by the Planteome project
When available the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources

The Plant Reactome increasingly includes curated regulatory and developmental pathways, which require more reference DNA and RNA sequence elements, in addition to the traditional protein-coding elements. These sequence elements are not included in Reactome ortho-inference at this time, although we are actively working to enhance the projection process to include these elements on projected pathways in future releases.