Gramene database build 43 released

The Gramene Team is pleased to announce its release #43. In collaboration with Ensembl Plants we are providing in this release:

• An updated barley genome assembly using POPSEQ data produced at the IPK. Based on original assembly produced by the International Barley Genome Sequencing Consortium, the update positionally anchors about three times as much DNA into chromosomes (410 Mbp vs. 1.17 Gbp), with a 4% increase in the number of anchored genes to the species "gene-ome".
• In addition to the existing (inter-varietal) bread wheat variation data from CerealsDB from last release, we have added more than 10 million 'inter-homoeologous' variations. These are positions that differ between homoeologous genes in the A, B and D sub-genomes. Plus the SIFT prediction of functional impact of non-synonymous mutations was calculated across all bread wheat variation datasets.
• A total of 71 million new tomato SNP variants covering 84 breeding varieties sequenced as part of the first release of the 150 Tomato Genomes ReSequencing Project making up for 300 million genotypes!

• Updated genome browser, database schema and API to Ensembl version 77. Domain annotation of protein coding genes for all species was updated with InterPro version 48.0 and InterProScan version 5. Updated gene, sequence and variation BioMarts.

• BioCyc-based pathway databases are now available from a virtual server hosted at iPlant. Pathway tools (ptools) software on this platform was updated to version 18.0. The pathway server on Gramene continues to exist in ptools ver 17.0, which is no longer supported by SRI ptools developers, and therefore will be eventually deprecated from the Gramene server. Stay tuned for Plant Reactome updates coming up in January 2015!

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