[Gramene-announce] Announcing Gramene database release #59

[Jaiswal, Pankaj - OSU]

Hi Everyone,

The Gramene Database (www.gramene.org) is pleased to announce 
its*Release #59 <http://gramene.org/release-notes-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.

*GENOMES:*

  * *New genomes*
      o /Triticum dicoccoides/
        <http://ensembl.gramene.org/Triticum_dicoccoides/Info/Index> (emmer
        wheat)
      o /Vigna radiata
        <http://ensembl.gramene.org/Vigna_radiata> (/mungbean/) /
  * *Updated genomes*
      o /Triticum aestivum
        <http://ensembl.gramene.org/Triticum_aestivum>/ (bread wheat)
  * *Retracted genome​*
      o /Cajanus cajan/(pigeonpea) was removed from this release,
        pending import corrections.

  * *New & Updated data*
      o The updated genomes include updated Whole Genome Alignments
      o Updated gene trees and homologies
      o New and updated synteny maps
      o Updated split gene predictions
        <ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/splitgenes/>
        from peptide comparative genomics
        <http://ensemblgenomes.org/info/data/peptide_compara>
      o Updated protein features
      o Updated BioMarts <http://ensembl.gramene.org/biomart/martview>
  * *Updated software*
      o Updated genome browser, database schema, Mart and API to Ensembl
        94 software <http://www.ensembl.info/2018/10/03/ensembl-94-is-out/>

*PATHWAYS*

  * *Website:*
      o New enhanced website http://plantreactome.gramene.org
      o 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
        <http://plantreactome.gramene.org/PathwayBrowser/#/R-ATH-5633340&SEL=R-ATH-5633332&PATH=R-ATH-2744345,R-ATH-2744343&DTAB=MT>.
      o The majority of the gene-gene interaction data is hosted in
        Plant Reactome. A part of it is pulled remotely fromEBI-Intact
        <https://www.ebi.ac.uk/intact/>and BAR <http://bar.utoronto.ca/>
        using the PSICQUIC
        <http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS>
        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.
      o Tricin biosynthesis
      o Lycopene catabolism
      o Oryzalyde A biosynthesis
      o Abscisic acid homeostasis
      o Reactive oxygen species (ROS) homeostasis
      o Generation of superoxide radicals
      o Removal of superoxide radicals
      o Valine degradation
      o Cysteine degradation
      o Recognition of fungal and bacterial pathogens and immunity response
      o Reproductive meristem phase change
      o Flower development
      o Floral bract development
      o 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
    <http://ensembl.gramene.org/Daucus_carota> /(carrot), /Vigna
    radiata/
    <http://ensembl.gramene.org/Vigna_radiata/Info/Index>/ (mung bean),/
    /Vigna angularis/
    <http://ensembl.gramene.org/Vigna_angularis> (adzuki bean) and
    /Triticum dicoccoides
    <http://ensembl.gramene.org/Triticum_dicoccoides/Info/Index> /(Emmer
    wheat). In addition, we have revised pathways for /Triticum
    aestivum/ <http://ensembl.gramene.org/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
    <http://plantreactome.gramene.org/PathwayBrowser/#TOOL=AT>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 <http://jaiswallab.cgrb.oregonstate.edu>

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