What’s coming in Ensembl 111 / Ensembl Genomes 58

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Ensembl 111 and Ensembl Genomes 58 are expected to be released in December 2023. Find out what’s coming in the new release, although we cannot guarantee everything listed here will make it into the final release.

Human

  • Updating human GRCh38 and GRCh37 variation data to dbSNP156
  • Probeset and motif mapping update for human GRCh38 assembly
  • MANE Select (v1.2) GRCh38 patch annotation
  • Final GRCh37 update. We will update:
    • Regulation data 
    • RefSeq (otherfeatures) data
    • Variation data- will include ~1billion dbSNP variants plus the latest data from all variant and phenotype association sources including ClinVar, OMIM and the NHGRI-EBI GWAS Catalog

Vertebrates

Updated genomes

  • Assembly update for Sheep (Ovis aries) reference – GCA_016772045.1 (ARS-UI_Ramb_v2.0) 
  • Assembly update for Cattle (Bos taurus) reference – GCA_002263795.3 (ARS-UCD1.3)

Regulatory annotation

  • New regulatory annotation for common carp and rainbow trout
  • Updated regulatory annotation, including enhancers, for pig and chicken
  • Updated regulatory annotation, including enhancers, for Atlantic salmon, European seabass and turbot

Metazoa

New species

Spruce gall adelgid (Adelges cooleyi) – GCA_023614345.1

Small hive beetle (Aethina tumida) – GCA_024364675.1

Parasitic wasp (Amblyteles armatorius) – GCA_933228735.1

Potter wasp (Ancistrocerus nigricornis) – GCA_916049575.1

Hunt’s bumblebee (Bombus huntii) – GCA_024542735.1

Montane Bumble Bee (Bombus vancouverensis nearcticus) – GCA_011952275.1

Desert ant (Cataglyphis hispanica) – GCA_021464435.1

Portuguese oyster (Crassostrea angulata) – GCA_025612915.2

Drywood termite (Cryptotermes secundus) – GCA_002891405.2

Grape phylloxera (Daktulosphaira vitifoliae) – GCA_025091365.1

Zebra mussel (Dreissena polymorpha) – GCA_020536995.1

Caddisflies (Glyphotaelius pellucidus) – GCA_936435175.1

Ichneumon wasp (Ichneumon xanthorius) – GCA_917499995.1

Caddisflies (Limnephilus lunatus) – GCA_917563855.2

Caddisflies (Limnephilus marmoratus) – GCA_917880885.1

Caddisflies (Limnephilus rhombicus) – GCA_929108145.2

Golden mussel (Limnoperna fortunei) – GCA_944474755.1

Bootlace worm (Lineus longissimus) – GCA_910592395.2)

Aster leafhopper (Macrosteles quadrilineatus) – GCA_028750875.1

Soft-shell clam (Mya arenaria) – GCA_026914265.1

Oribatid soil mite (Oppia nitens) – GCA_028296485.1

European flat oyster (Ostrea edulis) – GCA_023158985.1

Citrus red mite (Panonychus citri) – GCA_014898815.1

Blue-rayed limpet (Patella pellucida) – GCA_917208275.1

Common limpet (Patella vulgata) – GCA_932274485.1

South American locust (Schistocerca cancellata) – GCA_023864275.2

Grasshoppers (Schistocerca gregaria) – GCA_023897955.2

Vagrant locust (Schistocerca nitens) – GCA_023898315.2

Central American locust (Schistocerca piceifrons) – GCA_021461385.2

Grasshoppers (Schistocerca serialis cubense) – GCA_023864345.3

Varroa mite (Varroa jacobsoni) – GCA_002532875.1

Updated genomes

Dermacentor silvarum (Tick) assembly updated to GCA_013339745.2 

Rhipicephalus sanguineus (Tick) assembly updated to GCA_013339695.2

Removed genomes

Sand fly (Phlebotomus perniciosus) – older GCA_918844115.1

Pea aphid (Acyrthosiphon pisum) – older GCA_005508785.1 

Demosponge (Amphimedon queenslandica) – older GCA_000090795.1 

Lamp shell (Lingula anatina) – older GCA_001039355.1 

Tick (Dermacentor silvarum) – older GCA_013339745.1

Plants

New species

  • Wild soybean (Glycine soja) – GCA_004193775.2

Updated gene annotation

  • Cork oak (Quercus suber) 

Other updates and highlights

  • New Ensembl VEP plugin to integrate pre-calculated scores of variant effect on gene expression predicted by DeepMind’s Enformer
  • New Ensembl VEP plugin to integrate Open Targets Genetics Locus to Gene (L2G) scores with links out to the Open targets portal
  • Transcript length to be added to the output of the REST lookup endpoint
  • Limiting Metazoa species available in BioMart