What’s coming in Ensembl release 116 / Ensembl Genomes 63?

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Ensembl 116 and Ensembl Genomes 63 are expected in April 2026. Check out what we’re up to, although we can’t guarantee everything listed here will make it into the release. 

Special Notice

Ensembl 116 and Ensembl Genomes 63 will be the final releases on the current Ensembl site and platforms.

From the summer of 2026, all new data will only be available through the new Ensembl site. The site, ensembl.org, will redirect to the site currently hosted on beta.ensembl.org. 

Previous Ensembl versions are available via Ensembl Archives. Files from current and previous Ensembl versions are available via ftp.ebi.ac.uk/pub/ensembl/ and ftp.ebi.ac.uk/pub/ensemblgenomes/.

More information on future directions is available in our Ensembl 2026 Publication. Important information for programmatic access to Ensembl data is available in this blog post.

Please try the new site now at beta.ensembl.org. 

The new Ensembl site provides access to over 4700 genomes. There are over 4100 animal, 470 plant, and 100 fungal genomes ready to explore. We provide pangenomes for many species including human (565 haplotypes), barley (69 cultivars), and pig (27 breeds). Genomes from projects such as Darwin Tree of Life, the Human Pangenome Reference Consortium, the Vertebrate Genomes Project and the European Reference Genome Atlas, are regularly added. We are in the process of migrating our existing prokaryotic genomes, with a target of moving all ~36,000 by July 2026. Prokaryotic releases will be phased, with batches migrating from February 2026 onwards.

Human

A new transcript flag will be introduced on some human transcripts: “Ensembl Canonical Extended”. These flags will be applied to some transcripts that have been extended at their 5’ and 3’ ends. 

Vertebrates 

New Assemblies and/or Annotation:

We will add new cattle breed and donkey assemblies + annotations:

  • Bos taurus (Norwegian Red cattle) GCA_963921495.1
  • Equus asinus (donkey) GCA_041296235.2

We will add assemblies and annotations for new pig breeds:

  • Norwegian Landrace GCA_963921485.1  
  • Wuzhishan GCA_048338725.1  
  • Ghungroo GCA_046128825.1  
  • Large White GCA_044906105.1  
  • Isolate HJB GCA_044906185.1  
  • Banna miniature inbred pig GCA_041937265.1  
  • Juema GCA_040869115.1  
  • Korean minipig GCA_039654815.1  
  • Chenghua GCA_037447515.1  

Checks on annotation info, species image, and RNA-seq BAM files will be conducted and fixes introduced where needed for a number of vertebrate species. 

Fixes on existing annotation:

Fixes will be applied to update the stable ID of 2 annotations that had overlapping issues with other annotations (from the same species). This caused some access data points to not be reachable. By correcting the prefix of both annotations, the issue is now fixed.

  • Meishan (GCA_017957985.1) pig will have stable ID fixes only. The annotation has not been modified further.
  • Gadus morhua (GCA_010882105.1) cod will have stable ID fixes only. The annotation has not been modified further.

Plants

New Plant species:

  • Avena byzantina (Oat; GCA_910574625.1)
  • Avena magna x Avena longiglumis (Oat; GCA_947310255.1)
  • Avena occidentalis (Oat; GCA_947310975.1)
  • Avena sativa (Oat; GCA_947310285.1)
  • Avena sativa (Oat; GCA_947310875.1)
  • Avena sativa (Oat; GCA_947311775.1)
  • Avena sativa (Oat; GCA_947311525.1)
  • Avena sativa (Oat; GCA_947311085.1)
  • Avena sativa (Oat; GCA_947311555.1)
  • Avena sativa (Oat; GCA_947311355.1)
  • Avena sativa (Oat; GCA_947311365.1)
  • Avena sativa (Oat; GCA_947311235.1)
  • Avena sativa (Oat; GCA_947311915.1)
  • Avena sativa (Oat; GCA_947311225.1)
  • Avena sativa (Oat; GCA_947311165.1)
  • Avena sativa (Oat; GCA_951802355.1)
  • Avena sativa (Oat; GCA_947311155.1)
  • Avena sativa (Oat; GCA_951802365.1)
  • Avena sativa (Oat; GCA_947311135.1)
  • Avena sativa (Oat; GCA_947311925.1)
  • Avena sativa (Oat; GCA_947311345.1)
  • Avena sativa (Oat; GCA_947312425.1)
  • Avena sativa (Oat; GCA_947311295.1)
  • Avena sativa (Oat; GCA_947311595.1)
  • Avena sativa (Oat; GCA_951802345.1)
  • Avena sterilis TN1 (Oat; GCA_947313225.1)
  • Avena sterilis TN4 (Oat; GCA_947313515.1)

New assembly on present Plant species:

  • Gossypium raimondii (Peruvian cotton; GCF_025698545.1)

Updated Plant assemblies:

  • Cynara cardunculus var. scolymus (Artichoke; GCA_001531365.2)
  • Lactuca sativa (Garden lettuce; GCA_002870075.4)
  • Quercus suber (Cork oak; GCF_002906115.3)
  • Cajanus cajan (Pigeon pea; GCA_000340665.2)
  • Nymphaea colorata (Pocket water lily; GCF_008831285.2)
  • Solanum lycopersicum (Tomato; GCA_000188115.5)
  • Vigna unguiculata (Cowpea; GCF_004118075.2)

Plant variation databases dropped:

Due to their assembly being updated, the following variation databases will be dropped:

  • Cucumis sativa variation
  • Lactuca sativa variation  
  • Solanum lycopersicum variation

Plant funcgen databases dropped:

We will drop plant funcgen databases as they have not been maintained or updated for too long. 

Change on reference for Oat:

  • New reference
    • Avena sativa OT3098 (GCA_022788535.1)
  • Old reference, now displayed as a cultivar
    • Avena sativa Sang (GCA_910574605.1)

Compara

Vertebrates:

  • Pig comparative analyses have been updated to incorporate Meishan breed (GCA_017957985.1) plus 9 newly added Pig genomes, with a LastZ alignment of all 10 against the Pig reference genome. Each one has also been included in the Pig-breeds gene trees and EPO-Extended alignment, which now includes 30 pig breeds and wild relatives.
  • Updated Human self-alignment and self-synteny datasets.

Plants:

  • Oat pangenome protein trees
  • Four LastZ alignments:
    • Solanum lycopersicum Heinz1706 vs Arabidopsis thaliana
    • Solanum lycopersicum Heinz1706 vs Solanum tuberosum
    • Arabidopsis thaliana vs Nymphaea colorata Beijing-Zhang1983
    • Arabidopsis thaliana vs Gossypium raimondii GPD5lz
  • Two large protein clusters in Ensembl Plants have incomplete or missing homology data due to production constraints. To address this, we will make these clusters accessible via the gene families view. More information on this will be available in a blog post along with the 116 release. 

Metazoa:

  • Update of Metazoa and Protostomes protein-tree collections
  • Addition of two genomes to Protostomes protein trees:
    • Schmidtea mediterranea (Freshwater planarian, S2F18)
    • Steinernema hermaphroditum (Nematode, PS9179)

Microbes:

  • Updated protein trees for both Fungi and Protists
  • Twenty-five LastZ alignments in Fungi, each including at least one of Eremothecium gossypii FDAG1 or Magnaporthe oryzae
  • Nineteen Protists LastZ datasets involving Globisporangium ultimum DAOM BR144 (GCA_000143045.1)

Variation

Variation resources:

Vertebrate variation data on the Ensembl site has been updated to align with the latest EVA release version (8).

For the pig reference, we have enabled population frequency and genotype data through study (https://ftp.ebi.ac.uk/pub/databases/eva/PRJEB93975/), derived from variant calling work that we have now submitted to EVA.

We have added variation data support for 3 new species;

  • Anas platyrhynchos platyrhynchos
  • Camelus dromedarius
  • Clupea harengus

Ensembl VEP

Updating and expanding the Open Targets plugin to align with updates to the Open Targets platform, this adds support for annotating variants in the platform deriving from QTL studies alongside GWAS.

Expanding the existing EVE plugin to incorporate the latest popEVE scores.

New Ensembl VEP plugins:

  • To enable mitochondrial allele frequency data from gnomAD. 
  • To incorporate prediction scores from UniProt’s ProtVar for variant impact on folding, pockets, and stability.
  • To enable annotation with PromoterAI scores from Illumina.

Metazoa

Updated Metazoa assemblies:

  • Daphnia carinata (GCA_022539665.4)
  • Dermacentor andersoni (GCA_023375885.3)
  • Halyomorpha halys (GCA_000696795.3)
  • Hyalella azteca (GCA_000764305.3)
  • Lepeophtheirus salmonis (GCA_016086655.5)
  • Leptotrombidium deliense (GCA_003675905.2)
  • Loa loa (GCA_000183805.3)
  • Neodiprion pinetum (GCA_021155775.2)
  • Owenia fusiformis (GCA_903813345.2)
  • Patella vulgata (GCA_932274485.2)
  • Plodia interpunctella (GCA_027563975.2)
  • Pollicipes pollicipes (GCA_011947565.3)
  • Pristionchus pacificus (GCA_000180635.4)
  • Bactrocera oleae (GCF_042242935.1)
  • Cherax quadricarinatus (GCF_038502225.1)
  • Drosophila suzukii (GCF_043229965.1)
  • Onthophagus taurus (GCF_036711975.1)
  • Parasteatoda tepidariorum (GCF_043381705.1)
  • Penaeus vannamei (GCF_042767895.1)
  • Procambarus clarkii (GCF_040958095.1)

The following Metazoa species cores have been dropped:

  • Drosophila pseudoobscura – GCA_000001765.2 -> GCF_009870125.2
  • Hydra vulgaris – GCF_022113875.1 -> GCF_038396675.1
  • Lytechinus pictus – GCF_015342785.2 -> GCF_037042905.1
  • Mercenaria mercenaria – GCA_014805675.2 -> GCF_021730395.1
  • Necator americanus – GCA_000507365.1 -> GCF_031761385.1
  • Nematostella vectensis – GCA_000209225.1 -> GCF_932526225.1
  • Ostrea edulis – GCF_023158985.1 -> GCF_947568905.1
  • Schistosoma haematobium – GCF_000699445.2 -> GCF_000699445.3
  • Stylophora pistillata – GCA_002571385.1 -> GCA_002571385.2
  • Caenorhabditis remanei – GCA_000149515.1 -> GCF_010183535.1
  • Cherax quadricarinatus – GCF_026875155.2 -> GCF_038502225.1
  • Parasteatoda tepidariorum – GCA_000365465.3 -> GCF_043381705.1
  • Penaeus vannamei – GCA_003789085.1 -> GCF_042767895.1
  • Procambarus clarkii – GCA_020424385.2 -> GCF_040958095.1

Additional cores dropped:

The following cores have been dropped and replaced with the following assemblies:

  • Halyomorpha halys – GCF_000696795.2  -> GCF_000696795.3
  • Hyalella azteca – GCA_000764305.2  -> GCA_000764305.4
  • Lepeophtheirus salmonis – GCF_016086655.3  -> GCF_016086655.5
  • Owenia fusiformis – GCA_903813345.1 -> GCA_903813345.2
  • Pollicipes pollicipes – GCF_011947565.2 -> GCF_011947565.3   
  • Eufriesea mexicana  – GCF_001483705.1 -> GCF_001483705.2

Variation metadata:

  • MalariaGen URL links for A. gambiae have been removed because the Ag1000G app has been decommissioned and a new project, the Vector Observatory, has subsumed the data that was available via Python API.

Automation

All external references (xrefs) will be updated and InterProScan will be rerun on all species across Ensembl divisions.

Other updates and changes

The Ensembl 100 (Apr 2020), 101 (Aug 2020), 102 (Nov 2020) and 103 (Feb 2021) archives, and the Ensembl Genomes 49 (Dec 2020) archives are five years old and will be retired with the release of Ensembl 116 and Ensembl Genomes 63.