Gramene database build 45 released

Submitted by marcela.karey on Thu, 04/09/2015 - 15:50

The Gramene Team is pleased to announce its release #45. In collaboration with Ensembl Plants we are providing in this release:

  • Updated genome assembly and gene set for medicago and the wild rice Oryza meridionalis.

  • Whole genome alignments between Triticeae genomes using Assembly to Assembly Comparison, ATAC.

  • Whole genome alignments using LASTZ featuring Brassica oleracea and M. truncatula. See Plants Ensembl Compara analysis summary.

  • Split gene predictions for 39 plant genomes.

  • New genome browser tracks for Zea mays including predicted gene models (6a gene set) using MAKER-P software, genomewide DNA methylation patterns, long non-coding RNAs, and nascent transcriptome alignments (read more).

  • New RNA-Seq studies (leaf, root and panicle) for OGE genomes, including O. barthii, O. brachyantha, O. glaberrima, O. glumaepatula, O. meridionalis, O. nivara, O. punctata, O. rufipogon, O. sativa Japonica, and Leersia perrieri.

  • New links to gene annotations from AraPort and Expression ATLAS (see for example, pad4).

  • Synteny regions for bread wheat against O. sativa Japonica.

  • Peptide comparative genomics data across all species.

  • Enabled the assembly converter tool to allow conversion of Tomato 2.50 onto 2.40 coordinates.

  • Updated BLAST software, genome browser, database schema and API to Ensembl version 79.

  • Updated gene, sequence and variation BioMarts.

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