Ensembl 106 has been released!

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We are pleased to announce the release of Ensembl 106, and the corresponding release of Ensembl Genomes 53 featuring lots of new and updated data in this release including new and updated vertebrate, plant, worm and metazoan genomes as well as AlphaFold data for human, mouse, zebrafish, maize and soybean.

Genome assemblies and annotation for many new species are also being continuously added to the Ensembl Rapid Release genome browser.

Major data updates for human

New AlphaFoldDB data for human

EMBL-EBI and DeepMind have partnered to create the freely available AlphaFoldDB to provide protein structure predictions for 16 model organisms and 48 Global health proteomes (including bacteria, sporozoans and helminths). Ensembl 106 will see the integration of AlphaFold data for human as well as mouse, zebrafish, maize and soybean. This data will be available on the transcript tab and displayed in an AlphaFoldDB 3D widget. On top of the structure from AlphaFoldDB, you can visualise variants with SIFT and PolyPhen-2 pathogenicity predictions, plus Pfam domains and exons annotation.

View the human AlphaFold 3D structure in action here.

Predicted structure of the ENSP00000370113 protein viewed in the AlphaFoldDB 3D widget

Human frequency data updated to gnomAD 3.1

Human frequency data presented for variants in the Ensembl GRCh38 web pages has been updated from gnomAD genomes r3.0 to r.3.1.2. 

New genomes

We have added a whole set of new species to Ensembl Metazoa, including lots of ticks and parasitic worms from WormBase ParaSite.

Ticks:

Parasitic worms:

We also have three new species in Ensembl Plants:

New Assemblies and/or Annotation

Four updated genome assemblies, which were produced as part of the AquaFAANG project have been included in Ensembl 106:

  • Atlantic salmon (Salmo salar) assembly and gene set updated from ICSASG_v2 to Ssal_v3.1
  • Rainbow trout (Oncorhynchus mykiss) assembly and gene set updated from Omyk_1.0 to USDA_OmykA_1.1
  • European seabass (Dicentrarchus labrax) assembly and gene set updated from seabass_V1.0 to dlabrax2021
  • An additional Carp (Cyprinus carpio carpio) assembly (Cypcar_WagV4.0) and gene set update has been added
Common carp (Cyprinus carpio carpio), European seabass (Dicentrarchus labrax), Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar).

Metazoa:

We’ve also updated the genome assemblies and annotation for a number of species in Ensembl Metazoa. The updates from WormBase include hundreds of hand-curated gene models from the WormBase curator team:

Plants:

Ensembl 106 also sees assembly updates for two species in Ensembl Plants:

Other updates and changes

  • AlphaFoldDB data integrated for mouse, zebrafish, maize and soybean.
  • Retirement of Ensembl mobile site
  • Retirement of Ensembl 86 and Ensembl 87 archive sites
  • New VEP plugin to retrieve protein interaction data from IntAct is available for command line VEP 
  • ATAC-seq tracks from GENE-SWitCH added for pig
  • Wheat specific gene trees for different wheat cultivars and relatives
  • Human variant consequences in BioMart will only be available for MANE transcripts. Consequence data for other species remain unchanged.