We are pleased to announce the release of Ensembl 111, and the corresponding release of Ensembl Genomes 58 featuring a range of new Ensembl VEP plugins and tonnes of new and updated agricultural, fish, plant and metazoa species!
Genome assemblies and annotation for many new species are also being continuously added to the Ensembl Rapid Release genome browser.
We have added a whole host of new Ensembl VEP plugins that provide additional variant annotation from a range of sources:
The Open Targets Genetics team uses a Locus to Gene (L2G) model to prioritise likely causal genes from published GWAS trait-associated loci. The OpenTargets plugin integrates these results by variant and will be available through the Ensembl VEP web interface, command-line and REST platforms. The web interface links to variant-specific pages in the Open Targets portal for further information.
BayesDel is a deleteriousness meta-score for both coding and non-coding variants. The BayesDel plugin integrates precalculated scores into Ensembl VEP and will initially be available through the command-line interface only.
Varity predicts the pathogenicity of rare human missense variants. The Varity plugin will initially be available for Ensembl VEP command-line platform only.
The DosageSensitivity plugin reports when a variant overlaps a dosage sensitive gene, as identified by Collins et al. This plugin will initially be available through the Ensembl VEP command-line platform only.
DeepMind’s Enformer deep learning architecture predicts variant effects on gene expression. The Enformer plugin integrates precalculated scores and will initially be available through the Ensembl VEP command-line and REST platforms, with integration into the web interface planned for Ensembl 112.
The deNovo plugin is designed to be used to annotate a VCF when pedigree information is available (in a .ped file). It will highlight when a variant (or ref) allele has arisen de novo. This plugin is currently only available on the command-line platform.
SpliceVault is a new VEP plugin that predicts exon-skipping events and activated cryptic splice sites based on the most common mis-splicing events. This plugin is currently only available on the command-line platform.
The human variation data available in Ensembl has been updated to include dbSNP156, which represents over 1 billion individual variants.
The annotation on the human GRCh37 genome assembly has been updated to include dbSNP156 variants, the latest data from all variant and phenotype association sources including ClinVar, OMIM and the NHGRI-EBI GWAS Catalog, updated regulatory annotation and RefSeq data. The updated reference data will also be available in the Ensembl VEP cache, web tool and REST API.
Wild soybean (Glycine soja) – GCA_004193775.2
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
Cork oak (Quercus suber) updated gene annotation
Dermacentor silvarum (Tick) assembly updated to GCA_013339745.2
Rhipicephalus sanguineus (Tick) assembly updated to GCA_013339695.2
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