[Gramene-announce] Gramene database build 37 released

[Monaco, Marcela]

The Gramene Team is pleased to announce its release #37.  In collaboration with Ensembl Plants<http://plants.ensembl.org/> we are providing in this release:

  1.  The genome sequence of Medicago truncatula<http://www.gramene.org/Medicago_truncatula/Info/Index> (barrel clover), a model organism for legume biology.
  2.  The B73 Zea mays<http://www.gramene.org/Zea_mays/Info/Index> assembly and gene models updated to RefGen_v3 (AGPv3).  Researchers are able to do genome coordinate lifts between the maize B73 assembly version 2 and 3 using Ensembl's Assembly Converter Tool<http://www.gramene.org/tools.html>, which allows the conversion of a variety of annotation formats between different versions of a genome assembly.
  3.  The complete genome of Oryza punctata<http://www.gramene.org/Oryza_punctata/Info/Index> (wild rice species), which brings up to six the total number of complete Oryza genomes in Gramene.  Also, in an ongoing collaboration with the Oryza Genome Evolution<http://www.genome.arizona.edu/> project, we are releasing updated sequence of chr3s arms for other four Oryza species.
  4.  New alignments, repeats and noncoding RNA gene annotations for various Oryza species as provided by the Arizona Genomic Institute<http://www.genome.arizona.edu/>.<http://www.genome.arizona.edu/>
  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.  Updated maize variation data and microarray probe mapping.
  8.  Twenty-one new rice pathways in the Plant Reactome<http://plantreactome.oicr.on.ca> (beta version).
  9.  DNA and peptide comparative genomics to include all new species.
  10. Gramene genome browser, database schema and API updated to Ensembl version 71<http://useast.ensembl.org/info/docs/api/index.html>.
  11. New data for M. truncatula, Oryza spp and Z. mays in BioMart.

A complete description of the contents of this new release is available in our release notes<http://www.gramene.org/db/help?state=current_release_notes>.

Please let us know<http://gramene.org/db/feedback/send_feedback> if you have questions or suggestions.

Proud to serve the plant science community,

The Gramene Team

==
Marcela Karey Monaco, PhD
Cold Spring Harbor Laboratory