Gramene database build 48 released

The Gramene Team is pleased to announce its release #48. In collaboration with Ensembl Plants we are providing in this release:

• New ATLAS gene expression annotations

• New pairwise alignment between Solanum tuberosum and S. lycopersicum (build 2.50)

• New pairwise alignments between Theobroma cacao and: 1) Arabidopsis thaliana, 2) Oryza sativa, and 3) Vitis vinifera

• Extensive new pairwise alignments between the 12 OGE species, covering nearly 50 pairs of species, e.g. O. barthii vs. O. rufipogon, O. meridionalis vs. O. sativa, and O. barthii vs. Leersia perrieri

• Updated repeat identification across all plant species using RepBase (release 20140131) and PGSB-REdat (release 9.3p)

• Updated software, genome browser, database schema and API to Ensembl version 82

• Updated gene, sequence and variation BioMarts

• Updated protein domain information based on the latest InterProScan

• Updated pairwise alignments between Hordeum vulgare and: Aegilops tauschii, Brachypodium distachyon, and O. sativa

• Pathway Tools software update to version 19.0; new pathways dumps available

• Coming up: Two newly curated (rice) signaling pathways and three revised pathways in Plant Reactome

• Coming up: Twenty-five new species with projected pathways in The Plant Reactome, including two wild peanut ancestors (Arachis duranensis and Ar. ipaensis) and the "common bean" (Phaseolus vulgaris)

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