Gramene database build 42 released

Submitted by marcela.karey on Mon, 09/08/2014 - 13:08

The Gramene Team is pleased to announce its release #42. In collaboration with Ensembl Plants we are providing in this release:

New & updated genomes

  1. Six new genomes:
    • Theobroma cacao (cacao or "chocolate tree")
    • Ostreococcus lucimarinus (a unicellular green alga)
    • Leersia perrieri (a wild grass)
    • O. longistaminata (a wild rice)
    • Oryza rufipogon (brownbeard rice)
    • Brassica oleracea (species cultivars include kale, broccoli, cauliflower, cabbage, and Brussels sprouts)
  2. Updated assembly and gene build for Oryza barthii (wild rice).
  3. Chloroplast genomes for three wheat related genomes and mitochondrial genome for bread wheat.

New & updated pathways (Plant Reactome)

  1. New auxin signaling pathway in rice.
  2. Nine amino acid pathways updated by incorporating recent literature and genes & compartment re-assignments.
  3. New & updated orthology-based projections of rice pathways to 17 plant genomes in Gramene.

New & updated data

  1. Split gene predictions for 37 plant reference genomes based on the latest Ensembl Compara data.
  2. ncRNA annotation for bread wheat.
  3. Probes from the Affymetrix barley genome array aligned to barley.
  4. New maize variation data based on Panzea release 2.7.
  5. New sorghum variation data from Mace et al (2013).
  6. New bread wheat variation data from Axiom, iSelect and KASP array sets.
  7. Two transcriptome datasets from diploid einkorn wheat (T. monococcum cv DV92 and G3116) aligned to barley, bread wheat and Triticum urartu genomes using STAR.
  8. TriFLDB full-length cDNA sequences aligned to bread wheat genome.
  9. New whole genome alignments for bread wheat against barley.
  10. Updated gene-trees across 38 species.
  11. Updated GO term and gene name projection from Arabidopsis thaliana to all dicots.
  12. Updated gene, sequence and variation BioMarts.
  13. Updated genome browser, database schema and API to Ensembl version 76.

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