Announcing Gramene Database Release #62

The Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. The plant genome databases were built in direct collaboration with Ensembl Plants and the Plant Reactome database was produced in collaboration with the Reactome project. Core funding for the project is provided by the National Science Foundation, USA.

The Gramene team is pleased to announce its Release #62 containing updates in its Genome section, Pathway portal Plant Reactome and infrastructure. The genome portal hosts 67 plant genomes with six new species and the Plant Reactome, hosts pathways for 97 species. The Plant Reactome has extended orthology-based pathway projections for 15 new species; added 6 newly curated pathways; and updated 11 pathways in the reference species Oryza sativa (resulting in a total of 306 rice pathways). In the following sections we provide a summary of updates to the Gramene Knowledgebase.

Updates in the Genome Portal: Release #62 includes six new reference genomes and one updated genome. Overall, the Genome section providing access to information 96,607 GeneTree families comprising 2,146,774 individual genes from 67 plant genomes with 2,365,624 input proteins. 

• New genomes:

1. Robusta coffee (Coffea canephora): assembly and annotation GCA_900059795.1.
2. Hot pepper (Capsicum annuum): assembly and annotation GCA_000512255.2.
3. Global artichoke (Cynara cardunculus): assembly and annotation GCA_001531365.1.
4. Eragrostis tef (Eragrostis tef): assembly from ENA (GCA_000970635.1) and community annotation.
5. Durum wheat (Triticum turgidum, tetraploid AABB).
6. Common liverwort (Marchantia polymorpha): assembly and annotation GCA_003032435.1.

• Updated genomes:

1. Criollo cocoa, cacao or chocolate tree (Theobroma cacao): assembly update GCA_000208745.2.

• New & Updated data: 

1. New whole genome alignments for robusta coffee (Coffea canefora), hot pepper (Capsicum annuum), global artichoke (Cynara cardunculus), eragrostis tef (Eragrostis tef), durum wheat (Triticum turgidum), common liverwort (Marchantia polymorpha), and chocolate tree (Theobroma cacao); see summary here.
2. New synteny data for robusta coffee (Coffea canefora), hot pepper (Capsicum annuum), and chocolate tree (Theobroma cacao); see summary here.
3. Updated split gene predictions from peptide comparative genomics.
4. The Pan-taxonomic Compara set of gene trees was updated with two new plant species added (Marchantia polymorpha and Brachypodium distachyon), and one removed (Chondrus crispus).
5. Updated metadata for wheat EMS-induced mutations.
6. KASP marker information for the TILLING population is being displayed on the genetic variation pages for wheat.

• Updated software: Updated genome browser, database schema, and API to Ensembl 98 software.
• Synteny data: Here is a summary of all 66 synteny maps.

Updates in the Pathway Portal (Plant Reactome):

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 represents a significant expansion in the number of curated pathways, projected species, and associated inferred pathways, reactions and genes (~25% data increase). Plant Reactome now hosts pathway projections for 97 plant species (a list of available species are available in the content summary). Here, we provide a summary of Gramene Release 62 including website and coding updates, a list of new & updated pathways, information on new species, and projection statistics.

Curation of reference rice pathways

We have added 6 newly curated pathways, 11 updated pathways, and 2 "container" pathways, resulting in a total of 306 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 G1/S transition during mitosis. Our data model represents various steps of this event within the nucleoplasm (assembly of the pre-replication complex, activation of the pre-replication complex, and G1/S-specific transcription). Clickable elements allow the user to highlight a subset of reactions. For example, in this pathway, highlighted blue lines show "Activation of the pre-replication complex in G1/S transition":

Pathway Projection Statistics

We have extended orthology-based pathway projections for 15 new species. Plant Reactome now hosts pathway projections for 97 species ranging from unicellular autotrophs to higher plants ( for a list of available species in Plant Reactome  click here).

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. 

Infrastructure Updates

• Web Services: Gramene's web services page documents many ways to directly connect to and analyze our databases.
• Public MySQL Server

Our partner Ensembl Genomes offers a public, read-only MySQL server with copies of the species-specific and comparative genomic databases that we use. To use this with the mysql command-line client:

$ mysql -hmysql-eg-publicsql.ebi.ac.uk -P4157 -uanonymous

Please note that the versioning scheme used at this public database differs from ours; Gramene's release 62_98 is set as version 45_98 at Ensembl.

• Website and coding updates: 

  • The latest Plant Reactome pathway data has been re-indexed and made available via Gramene search.

  • This release of Plant Reactome 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.

​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 (2019). 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 (2019). Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res., gkz890, https://doi.org/10.1093/nar/gkz890
3. Tello-Ruiz MK, C.F. Marco , F.M. Hsu, R.S. Khangura, P. Qiao et al. (2019) Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLOS ONE 14(10): e0224086 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224086
4. Naithani S, P. Gupta, J. Preece, P. Garg, V. Fraser, L.K. Padgitt-Cobb, M. Martin, K. Vining and P. Jaiswal (2019). Involving community in genes and pathway curation. Database, 2019:1-8,  https://doi.org/10.1093/database/bay146