What’s coming in Ensembl release 109 / Ensembl Genomes 56?

Ensembl 109 and Ensembl Genomes 56 are expected in February 2023. Check out what we’re up to, although we can’t guarantee everything listed here will make it into the final release.

New Assemblies and/or Annotation


  • New assembly and gene set will be available for Donkey. This will be updated from ASM303372v1 (GCA_003033725.1) to ASM1607732v2 – GCA_016077325.2)
  • Horse assembly will be reannotated: A new gene set for EquCab3.0 (GCA_002863925.1) built will be available via new genebuild pipelines that use an updated transcriptomic data set
  • We will remove many low confidence CTCF features from our regulatory annotation for Human. The number of CTCF features will reduce from 175,885 in Release 108 to 101,734 in this release
  • New ATAC-seq tracks (peaks and signal) for four fish species will be available (Atlantic Salmon, European Seabass, Rainbow Trout and Turbot)



New species added:

Triticum aestivum Kariega (Wheat cultivar)

Avena sativa cv. Sang (Oat)

Avena sativa cv. Ot3098 (Oat)

Fraxinus excelsior (Ash tree)

Cajanus cajan (Pigeon pea)


New species added:

Acromyrmex echinatior – Panamanian leaf-cutter ant (GCA_000204515.1)

Apis dorsata – Giant honeybee (GCA_000469605.1)

Apis florea – Dwarf honeybee (GCA_000184785.2)

Bombyx mandarina – Wild silkworm (GCA_003987935.1)

Camponotus floridanus – Florida carpenter ant (GCA_003227725.1)

Daphnia pulex – Common water flea (GCA_021134715.1)

Daphnia pulicaria – Water flea (GCA_021234035.2)

Dufourea novaeangliae – Bee (GCA_001272555.1)

Echinococcus granulosus – Dog tapeworm (GCA_000524195.1)

Eufriesea mexicana – Orchid Bee (GCA_001483705.1)

Habropoda laboriosa – Southeastern blueberry bee (GCA_001263275.1)

Haliotis rubra – Blacklip abalone (GCA_003918875.1)

Haliotis rufescens – Red abalone (GCA_023055435.1)

Harpegnathos saltator – Indian jumping ant (GCA_003227715.2)

Hydra vulgaris – Swiftwater hydra (GCA_022113875.1)

Lepeophtheirus salmonis – Salmon louse (GCA_016086655.3)

Linepithema humile – Argentine ant (GCA_000217595.1)

Megachile rotundata – Alfalfa leafcutting bee (GCA_000220905.1)

Penaeus chinensis – Fleshy prawn (GCA_019202785.2)

Pogonomyrmex barbatus – Red harvester ant (GCA_000187915.1)

Pomphorhynchus laevis – Thorny-headed worm (GCA_012934845.2)

Schistosoma haematobium – Urinary blood fluke (GCA_000699445.2)

Stegodyphus dumicola – Social spider (GCA_010614865.2)

New species added from Wormbase: 

Clonorchis sinensis – Flatworm (GCA_003604175.2)

Echinococcus multilocularis – Flatworm (GCA_000469725.3)

Schmidtea mediterranea – Flatworm (GCA_002600895.1)

Haemonchus contortus – Barber pole worm (GCA_000469685.2)

We will remove the following genomes:

Anopheles atroparvus – Mosquito (GCA_000473505.1)

Daphnia magna – Freshwater flea (GCA_001632505.1)

Microbes (protists, fungi and bacteria):

  • Batch of 110 whole genome alignments in protists will be updated using LASTZ to align the genomes of 22 key species
  • A new resource will be created to represent molecular interactions involving genes in Ensembl; ranging from pathogen-host interactions to symbiotic relationships across microbes and other Ensembl species. This will be accompanied by a new display interface on our gene pages and REST API

Other updates and changes

  • Ensembl 91 archive will be retired with the new release
  • We will be retiring US West AWS mirror 
  • Perl 5.26 will be adopted as the minimum supported version for Ensembl. We will be going for Perl 5.26 (EoL) instead of Perl 5.3x to minimise the risks of the transition and to comply with the general consistency/stability approach of Ensembl.
  • There will be a new VEP plugin (UTR annotation) for Ensembl browser and REST API
  • SIFT and PolyPhen-2 missense variant pathogenicity predictions will be updated for vertebrate species. This may result in changes in predictions for some borderline variants.
  • We will update the Dog variant data to EVA release 3
  • VEP plugins and their dependencies will be included in the VEP docker image
  • External references will link GeneCards: We will display GeneCards links on Ensembl for humans only.