We are pleased to announce release 68 of Ensembl.
This release includes the new mouse assembly (GRCm38) as well as updated patches for the human assembly (GRCh37.p8). We introduce the Chinese softshell turtle (Pelodiscus sinensis) as a new species and update the Dog genome to CanFam3.1. The ground squirrel has been renamed to Ictidomys tridecemlineatus in line with recent taxonomic reassessments.
We have new Human structural variants from COSMIC release 59. Structural variation for Human and Mouse have been updated and new studies have been added. Sequence variation for Dog has been updated to dbSNP 131 and remapped to the new assembly. Mouse variations have also been remapped to the new assembly. Structural variation data are now available for Zebrafish (Danio rerio), Cow (Bos taurus) and Horse (Equus caballus). In addition, we have moved to using Sequence Ontology terms to describe consequences in Ensembl. The old Ensembl terms will still be available however we encourage users to use the new ones; we hope they become standard across all browsers.
New Mouse assembly
The high coverage assembly GRCm38 of the Mouse (Mus musculus) genome was produced by the GRC (Genome Reference Consortium). This new assembly is composed of 21 chromosomes and 22 unplaced scaffolds. Similar to the human genome assembly, the Genome Reference Consortium will be releasing additional sequence for GRCm38 in the form of minor releases (patches) in the future. Just as for the human genome, we will provide gene annotations and pairwise alignments for these regions.
The Chinese softshell turtle (Pelodiscus sinensis) assembly was produced by the RIKEN institute. The gene set was built using a mixed approach. Due to the lack of species specific sequences and the availability of RNASeq data for Chinese softshell turtle from RIKEN and BGI Institutes, the final gene set comprises of models based orthologous proteins from the vertebrate division of UniProtKB in addition to models from RNASeq data.
Website design update
In other news, starting with this release we will be incrementally refreshing the design of the Ensembl web template to improve its usability. The first stage involves minimal changes designed to make the pages tidier and more readable, without altering current functionality. Our only new design feature this release is an icon bar attached to the dynamic images, which replaces the “Export Image” button.