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 includes several new curated pathways, additional projected species, and associated inferred pathways, reactions and genes. Plant Reactome now hosts pathway projections for 106 plant species. Here, we provide a summary of Gramene Release 63 including website and coding updates, a list of new & updated pathways, information on new species, and projection statistics.

Recent Publications:

1. 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

Website and coding updates

This release utilizes an updated ortho-inference process, converted to Java from Perl and revised for efficiency. The script uses the rules previously set up for ortho-inference while containing minor adjustments to facilitate changes in the underlying Reactome data schema and take advantage of new features and functionalities present in our partner Reactome site.

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.

Curation of reference rice pathways

We have added 13 newly curated pathways, 8 updated pathways, and 1 "container" pathways, resulting in a total of 320 reference rice pathways. In this release, we focused on updates to rice metabolic pathways and curation of cell-cycle events.

Below: An example of newly curated cell-cycle pathways representing the synthesis of DNA. Clickable elements allow the user to highlight a subset of reactions. For example, in this pathway, highlighted blue lines show "DNA Replication Initiation":

We have extended orthology-based pathway projections for 9 new species (in bold below). 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.