Gramene database build 37 released

Submitted by admin on Thu, 06/13/2013 - 11:56

The Gramene Team is pleased to announce its release #37.  In collaboration with Ensembl Plants we are providing in this release:

  1. The genome sequence of Medicago truncatula (barrel clover), a model organism for legume biology.
  2. The B73 Zea mays assembly and gene models were also recently updated to RefGen_v3 (AGPv3).  We provide the Assembly Converter Tool developed by Ensembl, and which allows the conversion of a variety of annotation formats between different versions of a genome assembly.  Currently users are able to do genome coordinate lifts between the  maize B73 assembly version 2 and 3.
  3. The complete genome of Oryza punctata (wild rice species), which brings up to six the total number of complete and annotated Oryza genomes in Gramene.  Also updated the chr3s arms sequence of another four Oryza species.  This is an ongoing collaboration with the Oryza Genome Evolution project.
  4. New alignments, repeats and noncoding RNA gene annotations for various Oryza species provided by the Arizona Genomic Institute.
  5. Updates to the barley genome annotation including the calculation of the syntenic relationships generated by Ensembl Plants between barley and rice (MSU6), and barley and Brachypodium (v1.0), and new RNA-Seq derived data.
  6. New and updated split gene predictions for 23 reference genomes.
  7. Maize variation data and microarray probe mapping were also updated.
  8. Twenty-one new rice pathways in the Plant Reactome (beta version).
  9. Rebuilt DNA and peptide comparative genomics to include all new species.
  10. Gramene genome browser, database schema and API have been updated to Ensembl version 71.
  11. BioMart includes new data for M. truncatula, Oryza spp and Z. mays.

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.

Proud to serve the plant science community,

The Gramene Team