What’s coming in Ensembl 93 and Ensembl Genomes 40

Both Ensembl release 93 and Ensembl Genomes release 40 are scheduled for late June and early July 2018, respectively.

Included are a number of new genomes and genebuilds for vertebrates and plants (including leopard, Amur tiger, hagfish, pigeon pea, carrot and adzuki bean) and significant updates to the mouse GENCODE annotation and regulatory build. This release will also bring a new import of variants from dbSNP for human, and allele frequencies for dog variation data!

Read on to see further details of the highlights you can look forward to.

Ensembl 93

New assemblies, gene sets and annotations

  • First annotation of the Amur tiger (Panthera tigris altaica, PanTig1.0) genome
  • First annotation of the leopard (Panthera pardus, PanPar1.0) genome
  • First annotation of the inshore hagfish (Eptatretus burgeri, Eburgeri_3.2) genome
  • Updated Ensembl-Havana mouse GENCODE gene set (release M18)
  • New genome assembly set for cat (Felis_catus_9.0)
  • New regulatory build for mouse, increasing from 8 to 79 epigenomes and addition of over 100,000 new feature annotations
  • Annotation of lincRNAs for zebrafish and marmoset

Other updates and highlights

  • An update to our human variant dataset, resulting in a doubling of the number of available variants, many of which have allele frequency data from the gnomAD project
  • New genotype and frequency data available for dog imported from a from a study (EVA accession: PRJEB24066) which sequenced the full genomes of 238 dogs
  • New pairwise (LastZ) alignments for hagfish, cat, tiger and leopard
  • Updates to homology dataset for new cat and mouse genesets

Changes to REST API VEP endpoints

We’re improving the way that VEP reports frequency data via the REST API, but please be aware that this may affect the running of any scripts that utilise these endpoints. Further details will be included in the release blog.


Ensembl Genomes 40


New assemblies, gene sets and annotations

  • New genome assemblies for pigeon pea (Cajanus cajan), carrot (Daucus carota) and adzuki bean (Vigna angularis)
  • Updated genome assemblies for:
    • The grass Brachypodium distachyon (v3)
    • The green alga Chlamydomonas reinhardtii (v5.5)
    • The moss Physcomitrella patens (v3)
    • Poplar (Populus trichocarpa) (v3)
    • Foxtail millet (Setaria italica) (v2)

Other updates and highlights

  • Updated protein features and BioMarts


  • Updated genome assembly for Leishmania major
  • Updated gene trees and homologies, protein features and BioMarts


  • Updated gene trees and homologies, cross-references and BioMarts


  • No significant updates planned


  • No significant updates planned


For more details on the declared intentions please visit the Ensembl Genomes Release 40 Intentions (http://ensemblgenomes.org/info/release/40). Please note that these are intentions and are not guaranteed to make it into the releases.