We are pleased to announce the release of Ensembl 109, and the corresponding release of Ensembl Genomes 56. The release brings updates to donkey and horse assembly and lots of new plants and metazoa genomes. We have updated PolyPhen-2 and SIFT scores on the Variant Effect Predictor (VEP) and Ensembl browser. And we have a shiny new resource that shows molecular interactions involving genes in Ensembl; ranging from pathogen-host interactions to symbiotic relationships across microbes and other Ensembl species.

New and exciting genome assemblies and annotations for many new species are being continuously added to the Ensembl Rapid Release genome browser.

New Assemblies and/or Annotation

Vertebrates

• We have a new assembly and gene set for donkey. This has been updated from ASM303372v1 (GCA_003033725.1) to ASM1607732v2 (GCA_016077325.2)
• We have reannotated horse assembly: A new gene set for EquCab3.0 (GCA_002863925.1) built is now available via new GeneBuild pipelines that use an updated transcriptomic data set.
• We have removed many low confidence CTCF features from our regulatory annotation for human. The number of CTCF features has been reduced from 175,885 in Release 108 to 101,734 in Release 109.
• New ATAC-seq tracks (peaks and signal) for four fish species (Atlantic salmon, European seabass, rainbow trout and turbot) have been added.

Non-Vertebrates

Microbes (protists, fungi and bacteria):

• Batch of 110 whole genome alignments in protists has been updated using LASTZ to align the genomes of 22 key species.
• A new resource is now available to represent molecular interactions involving genes in Ensembl; ranging from pathogen-host interactions to symbiotic relationships across microbes and other Ensembl species. This is accompanied by a new display interface on our gene pages and REST API.

Plants:

New species added:

Triticum aestivum Kariega (Wheat cultivar)

Avena sativa cv. Sang (Oat)

Avena sativa cv. Ot3098 (Oat)

Fraxinus excelsior (Ash tree)

Cajanus cajan (Pigeon pea)

Metazoa:

New species added:

Acromyrmex echinatior – Panamanian leaf-cutter ant (GCA_000204515.1)

Apis dorsata – Giant honeybee (GCA_000469605.1)

Apis florea – Dwarf honeybee (GCA_000184785.2)

Bombyx mandarina – Wild silkworm (GCA_003987935.1)

Camponotus floridanus – Florida carpenter ant (GCA_003227725.1)

Daphnia pulex – Common water flea (GCA_021134715.1)

Daphnia pulicaria – Water flea (GCA_021234035.2)

Dufourea novaeangliae – Bee (GCA_001272555.1)

Echinococcus granulosus – Dog tapeworm (GCA_000524195.1)

Eufriesea mexicana – Orchid Bee (GCA_001483705.1)

Habropoda laboriosa – Southeastern blueberry bee (GCA_001263275.1)

Haliotis rubra – Blacklip abalone (GCA_003918875.1)

Haliotis rufescens – Red abalone (GCA_023055435.1)

Harpegnathos saltator – Indian jumping ant (GCA_003227715.2)

Hydra vulgaris – Swiftwater hydra (GCA_022113875.1)

Lepeophtheirus salmonis – Salmon louse (GCA_016086655.3)

Linepithema humile – Argentine ant (GCA_000217595.1)

Megachile rotundata – Alfalfa leafcutting bee (GCA_000220905.1)

Penaeus chinensis – Fleshy prawn (GCA_019202785.2)

Pogonomyrmex barbatus – Red harvester ant (GCA_000187915.1)

Pomphorhynchus laevis – Thorny-headed worm (GCA_012934845.2)

Schistosoma haematobium – Urinary blood fluke (GCA_000699445.2)

Stegodyphus dumicola – Social spider (GCA_010614865.2)

New species added from Wormbase: 

Clonorchis sinensis – Flatworm (GCA_003604175.2)

Echinococcus multilocularis – Flatworm (GCA_000469725.3)

Schmidtea mediterranea – Flatworm (GCA_002600895.1)

Haemonchus contortus – Barber pole worm (GCA_000469685.2)

We have removed the following genomes:

Anopheles atroparvus – Mosquito (GCA_000473505.1)

Daphnia magna – Freshwater flea (GCA_001632505.1)

Other updates and changes

• Ensembl 91 archive has been retired with the new release.
• We have retired the US West AWS mirror. Please refer to our blog for more information on how this may impact our US WEST users.
• We have adopted Perl 5.26 as the minimum supported version for Ensembl to comply with the general consistency/stability approach of Ensembl.
• There is an exciting new Ensembl VEP option for UTR annotation available through the  web and REST interfaces.
• Updated SIFT and PolyPhen-2 missense variant pathogenicity predictions for vertebrate species. Check out our blog on how this may result in changes in predictions for some borderline variants.
• Dog variation data from European Variation Archive release 3 is now available, in place of the previous dbSNP release. Less variants are now displayed due to the more strict QC applied by EVA.
• Ensembl VEP plugins and their dependencies have been included in the Ensembl VEP docker image.
• External references will now link GeneCards: We will display GeneCards links on Ensembl for humans only. 
• We have removed older discontinued microarrays from our oligo probe tracks, namely Affymetrix Human Genome U133A Array, Illumina HumanHT-12 v3, Illumina HumanHT-12 v4, Illumina HumanWG-6 v1 and Illumina HumanWG-6 v2.

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