Ensembl 114 and Ensembl Genomes 61 have been released

The Ensembl 114 and the corresponding release of Ensembl Genomes 61 is now live. This release brings an updated MANE set (v1.4) for the human GRCh38 assembly. In this release, existing data sets have been updated and there are lots of exciting new genomes across the different Ensembl sites including rodents, livestock, plant, microbial and metazoa species. Variation data has been updated to EVA release 6 and is available for 39 species

Regulation 

Regulation updates continue; there are now updated regulatory annotations for the human genome assembly GRCh37 (see Table 1 below).

Table 1: Summary of regulation updates in Ensembl release 114

Common name	Species	Assembly	Data updated
Human	Homo sapiens	GRCh37	Lifted over data: motif featuresregulatory annotation
		GRCh38	Updated regulatory annotation and motif features
Cattle	Bos taurus	ARS-UCD2.0 (GCA_002263795.4)	Regulatory annotationPrimary data tracks

The following data has been retired 

• External features from VISTA or FANTOM for Human & Mouse Other Regulatory Regions datasets in the Regulation BioMart.
• Probe mapping species; Caenorhabditis elegans, Saccharomyces cerevisiae, Ciona intestinalis

Human update

• The GENCODE Primary tag is now the default gene display in human and mouse. More information including how to enable other GENCODE tracks is available here.
• MANE has been updated to release v1.4.

New assemblies and/or annotation

Vertebrates

Rodents

• Updated Rat reference (GRCr8 automated annotation)
  • Rattus norvegicus (GRCr8)
• Updated annotations for The Mouse Genomes Project
  • Mus musculus c3hhej (C3H_HeJ_v3)
  • Mus musculus balbcj (BALB_cJ_v3)
  • Mus musculus dba2j (DBA_2J_v3)
  • Mus musculus nodshiltj (NOD_ShiLtJ_v3)
  • Mus musculus pwkphj (PWK_PhJ_v3)
  • Mus musculus wsbeij (WSB_EiJ_v3)
  • Mus musculus aj (A_J_v3)
  • Mus musculus 129s1svimj (129S1_SvImJ_v3)
  • Mus musculus fvbnj (FVB_NJ_v3)
  • Mus musculus cbaj (CBA_J_v3)
  • Mus musculus casteij (CAST_EiJ_v3)
  • Mus musculus c57bl6nj (C57BL_6NJ_v3)
  • Mus musculus akrj (AKR_J_v3)
  • Mus musculus nzohlltj (NZO_HlLtJ_v3)
  • Mus musculus lpj (LP_J_v3)
  • Mus spretus (SPRET_EiJ_v3)
• New annotations for The Mouse Genome Project
  • Mus musculus molossinus jf1msj (JF1_MsJ_v3)

Livestock and companion animals

• Updates
  • Bos taurus (Reference; ARS-UCD2.0)
• New annotations
  • Ovis aries (Ujimqin; ASM2241675v1)
  • Ovis aries (Texel; ASM2241677v1)

Change on reference for cat

• New annotation and new reference
  • F.catus_Fca126_mat1.0
• Old reference, now displayed as a breed (no changes to annotation)
  • Felis_catus_9.0 (Abyssinian breed)

Non-vertebrates

Plants

New genomes

Sphenostylis stenocarpa  (African yam bean; GCA_963425845.1)

Triticum aestivum Alchemy (wheat cultivar; GCA_951799155.1)

Hordeum vulgare pangenome (75 Barley genomes)

Updated species

Vitis vinifera PN40024 T2T assembly (Grapes, GCA_030704535.1)

Updated data for plant species

Wheat Watkins variation data

Fungi and protists

Several species in Ensembl Fungi and Protists have been updated with imports from VEuPathDB. Key Plasmodium species, causing the deadliest forms of malaria in primates and those used as models in rodents, and a number of important fungal pathogens are included in this update. A full list of species can be found on our websites. This change also aligns these data sets between VEuPathDB and Ensembl, enabling data analysis workflows to cross seamlessly between the two resources. We are very excited about the potential that increased data consistency can offer and are continuing to explore further opportunities. 

Metazoa

Updated annotations

Drosophila melanogaster (GCA_000001215.4, Flybase Release 6.54)

Anopheles albimanus (GCA_000349125.2)

Anopheles gambiae (GCA_000005575.1)

Anopheles quadriannulatus (GCA_000349065.1)

Glossina morsitans morsitans (GCA_001077435.1)

Rhodnius prolixus (GCA_000181055.3)

Schistosoma haematobium (GCA_000699445.3)

Assembly and annotation updated

Aedes albopictus (GCA_035046485.1)

Bombus terrestris (GCA_910591885.2)

Haemaphysalis longicornis (GCA_013339765.2)

Hyalomma asiaticum (GCA_013339685.2)

Ixodes persulcatus (GCA_013358835.2)

New assembly on existing species (assembly and annotation)

Anopheles albimanus (GCA_013758885.1)

Anopheles coluzzii (GCA_004136515.2)

Anopheles darlingi (GCA_943734745.1)

Anopheles gambiae (GCA_943734735.2)

Biomphalaria glabrata (GCA_947242115.1)

Bombyx mori (GCA_030269925.2)

Magallana gigas (GCA_963853765.1) – (formerly: Crassostrea gigas)

Entirely new species (assembly and annotation) 

Argiope bruennichi (GCA_947563725.1)

Chrysoperla carnea (GCA_905475395.1)

Culicoides brevitarsis (GCA_036172545.2)

Cydia pomonella (GCA_033807575.1)

Eurytemora carolleeae (GCA_000591075.2)

Gordionus sp. m RMFG-2023 (GCA_954871325.2)

Halichondria panicea (GCA_963675165.1)

Ischnura elegans (GCA_921293095.1)

Liolophura japonica (GCA_032854445.2)

Macrobrachium nipponense (GCA_015104395.2)

Platynereis dumerilii (GCA_026936325.1)

Variation

• Support for non tabix-indexed Ensembl VEP cache has been removed. Indexed VEP caches are more efficient and faster and should be used for all cases going forward.
• GRCh37 website now has a new track option available for gnomAD v4.1 variants. 
• Allele frequency data from the NIH AllOfUS study are now available as an option for Ensembl VEP on the website for GRCh38.
• New variation data from EVA release 6 is available for: 

Bos taurus (GCA_002263795.4)

Gallus gallus (GCA_01669948.1, GCA_000002315.5)

Equus caballus (GCA_002863925.1)

Felis catus (GCA_000181335.4, GCA_018350175.1)

Canis lupus familiaris (GCA_014441545.1)

Capra hircus  (GCA_001704415.1)

Danio rerio (GCA_000002035.4)

Ovis aries (GCA_016772045.1)      

Mus musculus  (GCA_000001635.9)

Rattus norvegicus (GCA_036323735.1)

Sus scrofa (GCA_000003025.6)

Bison bison bison (GCA_000754665.1)

Neovison vison (GCA_900108605.1)

Salmo salar (GCA_90523706.2)

Pan troglodytes (GCA_000001515.5)

Ficedula albicollis (GCA_000247815.2)

Macaca fascicularis (GCA_011100615.1)

Bos grunniens (GCA_005887515.1)

Dicentrarchus labrax (GCA_905237075.1)

Nomascus leucogenys (GCA_000146795.3)

Manacus vitellinus (GCA_001715985.2)

Parus major (GCA_001522545.2)

Seriola dumerili (GCA_002260705.1)

Cavia porcellus (GCA_000151735.1)

Coturnix japonica (GCA_001577835.1)

Macaca mulatta (GCA_003339765.3)

Anas platyrhynchos (GCA_008746955.1)

Microcebus murinus (GCA_000165445.3)

Oreochromis niloticus (GCA_001858045.3)

Peromyscus maniculatus bairdii (GCA_003704035.1)

Sander lucioperca (GCA_008315115.1)

Microtus ochrogaster (GCA_000317375.1)

Oryctolagus cuniculus (GCA_000003625.1)

Oncorhynchus mykiss (GCA_013265735.3)

Pongo abelii (GCA_002880775.3)

Meleagris gallopavo (GCA_000146605.4)

Chlorocebus sabaeus (GCA_000409795.2)

Callithrix jacchus (GCA_011100555.1)

Taeniopygia guttata (GCA_003957565.2)

Compara

• With a view to improving performance, we are changing the way some Cactus genome alignments are displayed. In selected Cactus image alignments, when accessing the alignment at a large scale, gene tracks will be hidden by default. When accessing the same alignment at a larger scale still, sequence tracks will be hidden by default. Hidden tracks may then be enabled as desired. More information in this blog post.

• In this release we have changed the way we generate TSV and XML homology files for the Ensembl FTP site: homologies between genes in multiple gene-tree collections can now be found in the homology files of each of those collections. For example, a homology between genes in the Mouse and Rat reference genomes would previously have been included in a concatenated homology file such as ‘Compara.113.protein_default.homologies.tsv.gz’ but not ‘Compara.113.protein_murinae.homologies.tsv.gz’. From release 114, such a homology will be in both files.

Other updates and changes

• The e98 archive (September 2019) is five years old and has been retired with the release of Ensembl 114.
• A reminder that Ensembl release 116 will be our last microarray probe mapping update. See here for more details.

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