Ensembl 116 and Ensembl Genomes 63 have been released!

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Ensembl 116 and Ensembl Genomes 63 are here! Highlights include new pig & cattle assemblies, 26 oat genomes, updated alignments and new Ensembl VEP plugins.

Special Notice – Ensembl Transition

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

All new data from this point will only be available through the new Ensembl site. In the next few months, the ensembl.org site will bring you to the site hosted on beta.ensembl.org. 

You will continue to have access to current Ensembl versions via Ensembl Archives, with the latest archives having extended tool support. The Ensembl USEast and Asia mirrors of the current main site will be retired over the transition period this summer.

More information on future directions is available in our Ensembl 2026 Publication. 

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

The new Ensembl site provides access to over 5200 genomes. There are over 4400 animal, 520 plant, 80 bacteria, 20 archaea and 150 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. Thousands more of our prokaryotic genomes will be added in the next few months.

Ensembl Transition webinar series: 

Join us at our upcoming webinars for an overview of what to expect over the Ensembl transition this summer: 

https://www.ebi.ac.uk/training/events/ensembl-transition

The webinars are free to join but registration is required.

Human

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

Vertebrates 

New Assemblies and/or Annotation:

We have added new cattle breed and donkey assemblies and annotations:

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

We have added 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 have been conducted and fixes introduced where needed for a number of vertebrate species. 

Fixes on existing annotation:

Fixes have been applied to update the stable ID of two 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 has stable ID fixes only. The annotation has not been modified further.
  • Gadus morhua (GCA_010882105.1) cod has stable ID fixes only. The annotation has not been modified further.

Regulatory annotation:

Regulation data for Atlantic salmon – Salmo salar (GCA_905237065.2) has been updated with two new ChIP-seq experiments (H3K27ac and H3K4me3) and an updated H3K27ac dataset. The revised regulatory annotation includes minor changes, primarily involving previously identified open chromatin regions that are now classified as enhancers.

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:

  • Cajanus cajan (Pigeon pea; GCA_000340665.2)
  • Cynara cardunculus var. scolymus (Artichoke; GCA_001531365.2)
  • Lactuca sativa (Garden lettuce; GCA_002870075.4)
  • Nymphaea colorata (Pocket water lily; GCF_008831285.2)
  • Quercus suber (Cork oak; GCF_002906115.3)
  • 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 have been dropped:

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

Plant funcgen databases dropped:

We have dropped 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 nine 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.
  • 10 fowl Cactus is now accessible via pairwise Cactus alignments.
  • Get to know yourself, with updated within-species genomic alignment and synteny datasets for Homo sapiens.

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 have made these clusters accessible via the gene families view. More information on this is available in this blog post.
  • Orthologue web views may include orthologues from outgroup species (e.g. Human).

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)
  • With the Caenorhabditis remanei genome assembly update (from GCA_000149515.1 to GCF_010183535.1) in this release, we’ve reloaded the WormBase WS269 nematode Cactus alignment, excluding the old C. remanei assembly and including Trichuris muris assembly TMUE3.0.

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)

Other:

  • We are centralising Cactus alignment HAL files to a single location — https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/ — and we recommend accessing these files from this location for the foreseeable future.
  • We have applied various tweaks and fixes to comparative web views, including:
    • display of paralogous genes in paralogous regions in the genomic alignment image view;
    • improved support for EPO-Extended alignments; and
    • better handling of species sets when viewing or exporting orthologue data.
  • We have updated the README for homology TSV files on Ensembl and Ensembl Genomes FTP sites, and added an example script ( get_hom_tsv.py) to illustrate how to access homology TSV data.
  • We have updated coverage statistics for 11 multiple genomic alignments, 319 pairwise genomic alignments, and 82 synteny datasets.

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 this 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

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

Expanded 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) have been updated and InterProScan has been 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 have been retired with the release of Ensembl 116 and Ensembl Genomes 63.