Plant Reactome is the pathway knowledgebase of Gramene. We utilize the Reactome pathway data model to represent plant metabolic, transport and signaling pathways, developmental processes, organ differentiation, and transcriptional regulatory networks. Manual biocuration is conducted in the reference species rice (O. sativa) and pathways are then projected via gene orthology to other species including single-cell photoautotrophs, lower plants, and higher plants.

Curation of reference rice pathways

We have added 2 newly curated pathways and 1 "container" pathway, resulting in a total of 309 reference rice pathways. These new pathways are for response to gravitopism stimuli.

• Response to stimuli: abiotic stresses and stimuli
•     Gravitropism under normal or artificial gravity environments
•         Regulation of seed germination and coleoptile growth under submergence and normal gravity environment
•         Regulation of lemma joints development and leaf angle by cytokinin

Black = existing pathway

Red = new container pathway

Green = new pathway

New added species

This release adds 10 new species. Plant Reactome now hosts pathway projections for 130 plant species. The gene homology-based projections were added for the following new species:

Brassica juncea (brown mustard)

Corymbia citriodora (lemon-scented gum)

Digitaria exilis (white fonio, fonio millet, hungry rice)

Echinochloa crus-gallis (barnyard grass)

Lolium perenne (rye grass)

Pisum sativum (pea)

Quercus lobata (valley oak)

Quercus suber (cork oak)

Secale cereale (rye)

Vigna unguiculata (cowpea or black-eyed pea)

Recent Publications:

1. 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
2. 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
3. Gupta P. et al. (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

4. Tello-Ruiz, Marcela Karey, Wei, Sharon, Olson, Andrew, Gupta, Parul, Naithani, Sushma, Chougule, Kapeel, Kumari, Sunita, Kumar, Vivek, D'Eustachio, Peter, Papatheodorou, Irene, Contreras-Moreira, Bruno, Jaiswal, Pankaj, Ware, Doreen (September 2021) Gramene's Reference Genomes and Comparative Resources for Horticultural Species. In: Abstracts of Presentations from American Society of Horticultural Science 2021 Annual Conference.

Analytical tools

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 106 projected species hosted by Plant Reactome.

We have extended orthology-based pathway projections for the additional 10 species from Ensembl. Plant Reactome now hosts pathway projections for 130 species ranging from unicellular autotrophs to higher plants.

*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.

Plant Reactome mirror at Powered-by-CyVerse

We continue to leverage the resources made available in the Powered-by-CyVerse virtual server environment by providing the Plant Reactome database mirror (https://plantreactome.cyverse.org) to facilitate training, education, and integration with the CyVerse platform and user community.