The Gramene Database build 52 is out!

The Gramene Team is pleased to announce its release #52 with 1,760,628 genes and 44 reference plant genomes. In collaboration with Ensembl Plants, we are providing in this release:

  • New data
    • The following data for the early release of B73 Zea mays RefGenV4 reference assembly are now available from Gramene's FTP site:
      • A preliminary gene ID association table for B73 Zea mays RefGenV3 <=> RefGenV4 (gene ID history)
      • Transposable element annotations (TEs in GFF)
      • Mitochondrial and chloroplast genome sequences (chrMt and chrPt from RefGenV3)
    • Mitochondrial and chloroplast chromosomes (from RefGenV3) were incorporated to the Zea mays (RefGenV4) genome browser
    • New gene model annotations for Arabidopsis thaliana (Araport 11)
    • Whole-genome alignment between the bread wheat (Triticum aestivum TGACv1) component genomes (restricted to homoeologues predicted in the Compara gene tree)
    • Whole-genome alignment between bread wheat and Brachypodium distachyon
    • Added two pairs of synteny for maize: Setaria italica vs. Zea mays, and Brachypodium distachyon vs. Zea mays
    • Nine newly curated rice reference pathways in Gramene's Plant Reactome, including Intracellular auxin transport, Response to cold temperature, Circadian rhythm, and Inflorescence development
    • New gene homology-based pathway projections for Beta vulgaris, Brassica napus, Syncechocystis pcc6803, and Trifolium pratense
  • Updated data and software
    • Updated protein features from InterPro and peptide comparative genomics
    • Updated gene and variation BioMarts
    • Updated software, genome browser, database schema and API to Ensembl 86 software
    • Two revised curated rice reference pathways: Polar auxin transport and Tryptophan biosynthesis
    • Updated pathway projections forTriticum aestivum (TGACv1) and Zea mays (RefGenV4) incorporating updated Compara orthology data

A complete description of the contents of this new release is available in our release notes.

Please let us know if you have questions or suggestions.

The Gramene Team