Announcing Gramene Database release #59 with new and updated plant genomes and pathways

Submitted by pankaj.jaiswal on Tue, 11/06/2018 - 14:24

The Gramene Team is pleased to announce its Release #59 with the Genome section providing access to information on 2,156,459 genes and 57 reference plant genomes. 1,860,691 protein-coding genes are organized in 96,500 gene families. The Plant Reactome -- Gramene's pathway portal -- introduces its new website http://plantreactome.gramene.org/ for improved user engagement and provides 14 new curated pathways. The gene orthology-based projection of pathways now extends to 78 species representing the plant tree of life.

Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species.

GENOMES:

PATHWAYS

  • Website:
    • New enhanced website http://plantreactome.gramene.org
    • Users can import/overlay gene-gene interaction data filtered by a confidence score (where available). This is done by enabling a threshold filter to be selected by the user in the Pathway Browser when viewing the interactor overlay. Try an example here.
    • The majority of the gene-gene interaction data is hosted in Plant Reactome. A part of it is pulled remotely from EBI-Intact and BAR using the PSICQUIC webservices.
  • New pathways: Following 14 new reference pathways were added. Browse them at http://plantreactome.gramene.org/PathwayBrowser/. We encourage users to suggest updates and critiques.
    • Tricin biosynthesis
    • Lycopene catabolism
    • Oryzalyde A biosynthesis
    • Abscisic acid homeostasis
    • Reactive oxygen species (ROS) homeostasis
    • Generation of superoxide radicals
    • Removal of superoxide radicals
    • Valine degradation
    • Cysteine degradation
    • Recognition of fungal and bacterial pathogens and immunity response
    • Reproductive meristem phase change
    • Flower development
    • Floral bract development
    • Seed development
  • Pathway projections: Plant Reactome now hosts pathway projections for 78 species ranging from unicellular autotrophs to higher plants. These include 4 new species: Daucus carota (carrot), Vigna radiata (mung bean), Vigna angularis (adzuki bean) and Triticum dicoccoides (Emmer wheat). In addition, we have revised pathways for Triticum aestivum (bread wheat), based on its recent genome update (IWGSC RefSeq v1.0).
  • Analysis tools: Plant Reactome provides pathway enrichment and species comparison tools for analyzing your omics data. The interaction overlays now include ~600,000 hosted gene-gene interactions for Arabidopsis thaliana.

Detailed release notes are available at http://gramene.org/release-notes-59.

The genome databases were built in direct collaboration with Ensembl Plants and the Plant Reactome database was produced in collaboration with the Reactome project.

Please let us know if you have questions or suggestions.

The Gramene Team
www.gramene.org