Gramene database build 44 released

Submitted by marcela.karey on Tue, 01/20/2015 - 16:43

The Gramene Team is pleased to announce its release #44. In collaboration with Ensembl Plants we are providing in this release:

  • A new assembly for bread wheat. This was achieved by ordering the existing IWGSC Chromosome Survey Sequence (CSS) contigs into chromosomal pseudomolecules. This was accomplished using anchoring data from high marker density population sequencing (POPSEQ) from the Institute of Plant Genetics and Crop Plant Research (IPK) at Gatersleben (Mascher et al, 2013) and processed at The Genome Analysis Center. The resulting set of chromosomes were combined with the IWGSC's BAC by BAC assembly and annotation of chromosome 3B, generated by the [GDEC](http://www6.clermont.inra.fr/umr1095_eng0 group at INRA (Paux et al, 2008), which replaces the CSS-derived assembly and annotation of 3B. Ensembl Plants projected the contig level gene models (MIPS version 2.2) to the chromosome pseudomolecules using their Assembly Converter Tool. The MIPS genes are viewable as an additional track on 3B, where possible. The anchoring process (with the exception of 3B) placed 1,290,751 CSS contigs into chromosomal pseudomolecules for a total length of 4,237,502,413 bp. Ensembl Plants also incorporated 261,251 unanchored scaffolds, with cumulative length of 1,307,508,887 bp.

  • New marker and variation data for barley including new POPSEQ marker and variation data from the IPK with new variation identifiers from the transPLANT variation archive.

  • New KeyGene markers for Brassica rapa.

  • New whole genome alignment data for B. oleracea against B. rapa.

  • Updated genome browser, database schema and API to Ensembl version 78. Updated gene, sequence and variation BioMarts.

  • Plant Reactome pathways for 33 new species, including maize, wheat, soybean, Arabidopsis, banana, Brassicas, and numerous wild species related to rice. These pathways were annotated based on orthology projections from curated pathways in rice. In addition, this release of the Plant Reactome includes 16 newly curated and 1 updated rice pathways.

  • BioCyc databases were moved to a website powered by the iPlant collaborative. The Pathway tools software was updated to version 18.0 and Cyc databases were updated if a newer version was available.

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