Ensembl 112 has been released.

We are pleased to announce the release of Ensembl 112, and the corresponding release of Ensembl Genomes 59. We have some exciting new fish species, many more drosophila species and some incredible VEP updates.

Regulation

We are transitioning our regulatory annotation over the next few releases to be based on open chromatin, rather than genomic segmentation of histone marks. As a necessary step, we have removed segmentation data and tracks from human and mouse regulatory annotation in this release. 

In addition, our promoters now align with the 5’ ends of known transcripts (specifically 10 bp downstream). Our feature annotation GFF file on the FTP site includes the gene(s) associated with each promoter.

New Assemblies and/or Annotation

Vertebrates

Amphiprion ocellaris (Clown anemone fish) – GCA_022539595.1

Anabas testudineus (Climbing perch) – GCA_900324465.3

Astatotilapia calliptera (Eastern happy) – GCA_900246225.5

Clupea harengus (Atlantic herring) – GCA_900700415.2

Denticeps clupeoides (Denticle herring) – GCA_900700375.2

Electrophorus electricus (Electric eel) – GCA_013358815.1

Esox lucius (Northern pike) – GCA_011004845.1

Gasterosteus aculeatus (Three-spined stickleback) – GCA_016920845.1

Ictalurus punctatus (Channel catfish) – GCA_004006655.3

Oncorhynchus tshawytscha (Chinook salmon) – GCA_018296145.1

Oreochromis aureus (Guangdong) – GCA_013358895.1

Parambassis ranga (Indian glassy fish) – GCA_900634625.2

Periophthalmus magnuspinnatus (Bony fishes) – GCA_009829125.3

Pygocentrus nattereri (Red-bellied piranha) – GCA_015220715.1

Additional strains have been added for the following fish species:

Gadus morhua (Atlantic cod):

  • Celtic sea – GCA_010882105.1

Salmo salar (Atlantic salmon):

  • North American Atlantic salmon – GCA_021399835.1
  • Brian – GCA_923944775.1
  • European origin – GCA_931346935.2

Gasterosteus aculeatus (three-spined stickleback):

  • Marine – GCA_006232285.1
  • Marine – GCA_006232265.1
  • Freshwater – GCA_006229185.1

Non-Vertebrates

Plants:

New Genomes

Vicia faba (Broad bean) – GCA_948472305.1

Aegilops umbellulata (Umbel goatgrass) – GCA_032464435.1

Updated species

Manihot esculenta (Cassava) – GCA_001659605.2

Medicago truncatula (Barrel Medic) – GCA_003473485.2

Metazoa:

New Drosophila Pangenome

We have introduced a new Drosophila genus wide pangenome which incorporates resources from the main metazoa site.

This pangenome covers a whopping 36 species of Drosophila and 4 outgroup species. These species are currently hosted on both Ensembl metazoa and Rapid Release

New species:

Bactrocera neohumeralis (GCA_024586455.2) 

Cherax quadricarinatus (GCA_026875155.2) 

Coremacera marginata (GCA_914767935.1) 

Ctenocephalides felis (GCA_003426905.1) 

Daphnia carinata (GCA_022539665.3) 

Diaphorina citri (GCA_000475195.1) 

Drosophila albomicans (GCA_009650485.2) 

Drosophila arizonae (GCA_001654025.1) 

Drosophila biarmipes (GCA_025231255.1) 

Drosophila bipectinata (GCA_000236285.2) 

Drosophila busckii (GCA_011750605.1) 

Drosophila elegans (GCA_000224195.2) 

Drosophila eugracilis (GCA_018153835.1) 

Drosophila ficusphila (GCA_018152265.1) 

Drosophila guanche (GCA_900245975.1) 

Drosophila gunungcola (GCA_025200985.1)

Drosophila hydei (GCA_003285905.2) 

Drosophila innubila (GCA_004354385.1) 

Drosophila kikkawai (GCA_018152535.1) 

Drosophila mauritiana (GCA_004382145.1) 

Drosophila miranda (GCA_003369915.2) 

Drosophila navojoa (GCA_001654015.2) 

Drosophila obscura (GCA_018151105.1) 

Drosophila rhopaloa (GCA_018152115.1) 

Drosophila santomea (GCA_016746245.2) 

Drosophila subobscura (GCA_008121235.1) 

Drosophila subpulchrella (GCA_014743375.2) 

Drosophila suzukii (GCA_013340165.1)

Drosophila takahashii (GCA_018152695.1) 

Drosophila teissieri (GCA_016746235.2) 

Eriocheir sinensis (GCA_024679095.1) 

Halyomorpha halys (GCA_000696795.2) 

Homarus gammarus (GCA_958450375.1) 

Hydractinia symbiolongicarpus (GCA_029227915.2) 

Lytechinus pictus (GCA_015342785.2) – 

Machimus atricapillus (GCA_933228815.1)  

Melanaphis sacchari (GCA_002803265.2) 

Microctonus aethiopoides (GCA_030272655.1)  

Microctonus aethiopoides (GCA_030272935.1)  

Microctonus aethiopoides (GCA_030347275.1)  

Microctonus hyperodae (GCA_030347285.1) 

Myopa tessellatipennis (GCA_943737955.1) 

Octopus bimaculoides (GCA_001194135.2) 

Paramacrobiotus metropolitanus (GCA_019649055.1) 

Pecten maximus (GCA_902652985.1) 

Tribolium madens (GCA_015345945.1) 

Uloborus diversus (GCA_026930045.1) 

Updated genomes:

Drosophila ananassae (GCA_017639315.2) 

Drosophila erecta (GCA_003286155.2)

Drosophila grimshawi (GCA_018153295.1)

Drosophila mojavensis (GCA_018153725.1) 

Drosophila persimilis (GCA_003286085.2) 

Drosophila pseudoobscura (GCA_009870125.2) 

Drosophila sechellia (GCA_004382195.2)

Drosophila simulans (GCA_016746395.2) 

Drosophila virilis (GCA_003285735.2) 

Drosophila willistoni (GCA_018902025.2) 

Drosophila yakuba (GCA_016746365.2) 

The following outdated genomes have been removed:

Daphnia pulex (GCA_000187875.1)

Hydra vulgaris (GCA_000004095.1)

Octopus bimaculoides  (GCA_001194135.1)

Rhipicephalus sanguineus (GCA_013339695.1) We will retain the V2 assembly version (GCA_013339695.2) 

Other updates and changes

  • A new Ensembl VEP option has been added to predict the molecular consequence variants on human GRCh38 open reading frames found in long non-coding RNAs (lncRNAs) and untranslated regions (UTRs) of protein-coding genes, as described in Mudge et al.
  • The Ensembl VEP web and REST interfaces have been updated to use the dbNSFP commercial data release.
  • We have now retired Ensembl Archive 95 and 96 with this release.

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