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.

This release is a maintenance release with one new addition. The gene homology-based projections were added for the version #5 of the reference maize genome (Zea mays version v5). Plant Reactome now hosts pathway projections for 106 plant species.

Recent Publications:

1. Naithani S, D.A. Dikeman, P. Garg, N. Al-Bader, and P. Jaiswal (2021). Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily. PeerJ 9:e11052, doi:10.7717/peerj.11052
2. Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece S, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D’Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, and Ware D. (2021). Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research 49(D1): D1452–D1463. 10.1093/nar/gkaa979
3. Naithani S., P. Gupta, J. Preece, P. D'Eustachio, J. Elser, J. Kiff, P. Garg, D.A. Dikeman^$, A.J. Olson, S. Wei, M.K. Tello-Ruiz, J. Cook, A. Fabregat, T. Cheng, E. Bolton, A.F. Muñoz-Pomer, S. Mohammed, I. Papatheodorou, L. Stein, D. Ware, and P. Jaiswal (2020). Plant Reactome: A knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz996.
   

2. Howe K.L., B. Contreras-Moreira, N. De Silva, G. Maslen, W. Akanni, J. Allen, J. Alvarez-Jarreta, M. Barba, D.M. Bolser, L. Cambell, M. Carbajo, M. Chakiachvili, M. Christensen, C. Cummins, A. Cuzick, P. Davis, S. Fexova, A. Gall, N. George, L. Gil, P. Gupta, K. E. Hammond-Kosack, E. Haskell, S. E. Hunt, P. Jaiswal, S. H. Janacek, P. J. Kersey, N. Langridge, U. Maheswari, T. Maurel, M. D. McDowall, B. Moore, M. Muffato, G. Naamati, S. Naithani, A. Olson, I. Papatheodorou, M. Patricio, M. Paulini, H. Pedro, E. Perry, J. Preece, M. Rosello, M. Russell, V. Sitnik, D. M. Staines, J. Stein, M. K. Tello-Ruiz, S. J. Trevanion, M. Urban, S. Wei, D. Ware, G. Williams, A. D. Yates, P. Flicek (2020). Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res., gkz890, https://doi.org/10.1093/nar/gkz890

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 Zea mays version 5. Plant Reactome now hosts pathway projections for 106 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.