Announcing Gramene Database release #63 with 26 new plant genomes!

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 Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 1907-21000-030-00D), and the National Science Foundation (NSF IOS-1127112).

The Gramene team is pleased to announce its Release #63 containing updates in its Genomes section, Pathway portal Plant Reactome, and overall infrastructure. The genome portal hosts 93 plant genomes with 26 new species, and the Plant Reactome hosts pathways for 97 species. We have added new SNP variation datasets for sunflower, Golden apple, and durum wheat; and increased our comparative genomics data collection to comprise 122,947 gene family trees, 382 pairwise whol-genome alignments, and 83 synetny maps. 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

  • New genomes:
  1. Arabis alpina (alpine rock-cress)
  2. Camelina sativa (camelina, gold-of-pleasure or false flax)
  3. Cannabis sativa (cannabis or marijuana)
  4. Citrullus lanatus (watermelon)
  5. Cucumis melo (cantaloupe or muskmelon, smooth-skinned)
  6. Nymphaea colorata (a tropical water lily)
  7. Prunus dulcis (almond)
  8. Rosa chinensis (China or Chinese rose; Bengal rose, crimson or beauty)
  9. Setaria viridis (wild or green foxtail millet, green bristlegrass )
  10. Citrus clementina (clementine; citrus fruit hybrid between mandarin and sweet orange)
  11. Ipomoea triloba (morning glory, a relative of sweet potato )
  12. Malus domestica (Golden apple)
  13. Olea europaea sylvestris (wild olive tree)
  14. Pistacia vera (pistachio)
  15. Prunus avium (sweet cherry)
  16. Ananas comosus (pineapple)
  17. Eragrostis curvula (weeping lovegrass)
  18. Saccharum spontaneum (a sugar-poor relative of sugarcane)
  19. Chara braunii (Braun's stonewort, an ecorticated streptophyte algae)
  20. Hordeum vulgare subsp. GoldenPromise (barley var. GoldenPromise)
  21. Theobroma cacao subsp. Matina 1-6 (Matina cocoa, cacao or chocolate tree)
  22. Triticum aestivum subsp. Cadenza
  23. Triticum aestivum subsp. Claire
  24. Triticum aestivum subsp. Paragon
  25. Triticum aestivum subsp. Robigus
  26. Triticum aestivum subsp. Weebill
  • Updated genomes:
  1. Renamed almond gene names.
  • New & updated data: 
  1. Added new variation data for sunflower, apple and durum wheat.
  2. New whole-genome alignments, see summary here.
  3. New synteny maps, see summary here.
  4. Updated split gene predictions from peptide comparative genomics.
  5. A total of 122,947 GeneTree families were constructed comprising 2,875,432 individual genes from 93 plant genomes with 3,169,866 input proteins.
  • Updated software: 
  1. Updated genome browser, database schema, and API to Ensembl 101 software.

 

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.

New pathways Updated pathways
G1 Phase
    - G1/S Transition
        - Assembly of pre-replication complex
        - Activation of pre-replication complex
        - G1/S-specific transcription
OsNAC5 transcription network involved in drought and high salinity tolerance
Allantoin degradation
Aminopropanol biosynthesis
Ascorbate biosynthesis
Vitamin E biosynthesis
Arginine biosynthesis
Asparagine biosynthesis
Beta-alanine biosynthesis I
Beta-alanine biosynthesis III
Tyrosine degradation I
Ammonia assimilation cycle
Ureide biosynthesis

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":

Sample curated pathway r62

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. 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. Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Manuscript accepted by NAR Database (2021).
  2. 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.
  3. 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
  4. Tello-Ruiz MK, C.FMarco , F.MHsu, R.SKhangura, 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
  5. 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