We’re pleased to announce the release of Ensembl 99, and the corresponding release of Ensembl Genomes 46. Along with updates of human gene annotation and variation data, we have a menagerie of new and updated vertebrate species in Ensembl plus a whole set of new plants, mosquitos and flies in Ensembl Genomes.
Human and Mouse
Human and mouse gene annotation
Release 99 brings us up to GENCODE 33 on our human genome annotation and GENCODE M24 for mouse. As always, this brings a number of new genes and changes to existing ones.
Human variation data
We have updated our human GRCh38 variation database, importing data from the latest version of dbSNP (dbSNP153).
The COSMIC team have changed how they name somatic mutations and this is reflected in Ensembl. New ‘COSV’ identifiers have replaced the traditional ‘COSM’ identifiers, but the old names are still searchable as variant synonyms, so you’ll still be able to find your variant!
We’ve added a whopping 38 new species and two dog breeds in Ensembl 99 as well as four updated genome assemblies.
Thirteen of the new assemblies have been produced by the Vertebrate Genome Project (VGP), and part of Ensembl’s mission is to provide gene annotation for the genome assemblies produced by this long-term global collaboration.
For Ensembl 99, this includes updated genome assemblies for zebra finch (bTaeGut1_v1.p), Asian bonytongue (fSclFor1.1) and fugu (fTakRub1.2) as well as debuts for Canada lynx, greater horseshoe bat, golden eagle, kakapo, jewelled blenny, pinecone soldierfish, live sharksucker, orbiculate cardinalfish, gilthead seabream and the river trout, which is also from the Sanger 25 Genomes Project.
The new and updated species in Ensembl 99 from the Vertebrate Genomes Project (VGP)[/caption]
Fish with four rounds of whole genome duplication
We have also annotated a number of fish that have all undergone a fourth round of whole genome duplication which includes the golden-line barbel, blind barbel and horned golden-line barbel, as well as three strains of the common carp – the German mirror, Hebao red (from Wuyan in China) and the Hunaghe (from the Hunag He river).
This group of fish also includes the Atlantic salmon, which is part of the AquaFAANG project, and displayed along with variation data from EVA. Stay tuned for even more salmonid genomes to be released in Ensembl 100!
We have added two new dog breeds – the Great Dane and Basenji.
Even more mammals, birds, fish and reptiles…
Plus, six more mammalian genome assemblies: Siberian musk deer, Chacoan peccary, sperm whale, meerkat, Arabian camel and domestic yak.
Nine more bird genome assemblies: Gouldian finch, yellow-billed parrot, burrowing owl, African ostrich, swan goose, Indian peafowl, Eurasian sparrowhawk, golden pheasant and ring necked pheasant.
The blue tilapia, round goby and an updated assembly for the Nile tilapia (O_niloticus_UMD_NMBU).
And four new reptiles: Komodo dragon, common wall lizard, Eastern brown snake and three-toed box turtle.
The number of species in Ensembl Plants continues to grow as we have added four new plant genome assemblies: sweet cherry (Prunus avium), clementine (Citrus clementina), morning glory (Ipomoea triloba) and wild sugarcane (Saccharum spontaneum).
We have also added genetic variants from a diversity panel of durum wheat (Triticum turgidum) including the 35K, 90K, 820K and TaBW280K data sets.
A total of 35 new genome assemblies have been imported from Vectorbase into Ensembl Metazoa, including:
- 18 new Anopheles mosquito species
- an update from the L3 to L5 assembly for Aedes aegypti
- the vector of Zika virus Aedes albopictus
- six Tsetse fly species
- two Sand fly species
- the freshwater snail vector of schistosomiasis (Biomphalaria glabrata)
- the common bedbug (Cimex lectularius)
- the Lyme disease tick (Ixodes scapularis)
- common house fly (Musca domestica)
- stable fly (Stomoxys calcitrans)
Assemblies for common Anopheles laboratory strains for An. sinensis (sinensis and China), An. stephensi (SDA-500 and Indian) and An. coluzzii (Ngousso and Mali-NIH)
Gene synonyms will be added as a filter/attribute to use in BioMart queries.
Archived releases for all non-vertebrate site
Finally, we are creating Ensembl Genomes 45 archive sites for all of the non-vertebrate divisions: plants, metazoa, protists, fungi and bacteria.