Ensembl 90 has been released!

Ensembl 90 is now live and it’s absolutely massive! Read on to find out why:

New species and annotation

Ensembl 90 is our biggest release ever in terms of species.

Images of the new rodents
New/updated rodents in Ensembl 90: Kangaroo rat (updated genes), Guinea pig (updated genes), Golden hamster (new), Degu (new), Damara mole rat (new), Brazilian Guinea pig (new), Algerian mouse (new), Lesser Egyptian jerboa (new), Ryukyu mouse (new; imported annotation), Prairie vole (new), Naked mole rat (new; two assemblies available), Chinese hamster ovary (new; imported annotation), Northern American deer mouse (new), Long-tailed chinchilla (new), Shrew mouse (new; imported assembly), Upper Galilee mountains blind mole rat (new), Squirrel (updated genes) and Chinese hamster (new).

We’ve got 19 new or updated rodent genomes. Of these, sixteen were annotated with our new clade-based system, which makes use of the similarity between species’ genomes to automatically annotate genes onto the homologous regions:

We have also imported three new rodent genomes and their annotation:

This is the first ever Ensembl release where we’ve imported annotation from external resources, but our rigorous quality control makes us confident that these species’ annotation will meet the high standard expected of Ensembl genes. It’s also the first time we’ve supported more than one genome assembly per species (naked mole rat and Chinese hamster) in one Ensembl database, which will allow you to continue to work with your preferred assembly, within the Ensembl framework. We plan to continue to import high quality gene sets, where available, and to use our quicker clade-based annotation, so expect lots more new genomes appearing in future Ensembl releases.

Aside from rodents, we’ve got a new pig genome assemblySscrofa11.1 from the Swine Genome Sequencing Consortium. The assembly is created from a single Duroc sow, named TJ Tabasco. The genome was annotated using species specific RNA-Seq data, PacBio long reads and cDNAs, as well as proteins from related vertebrates.

We also have updates to our human, mouse and zebrafish gene sets. This brings us to human GENCODE 27, updating to the human genome patch version GRCh38.p10 with the latest updates from the Ensembl automatic and Havana manual annotation, and mouse GENCODE M15, with the latest Ensembl and Havana genes. Zebrafish annotation incorporates new gene models from RNA-seq and adds pri-miRNAs to the other features database.

Variation data

We have updates to our variation data coming in for humanCOSMIC 81 somatic variants, HGMD 2016.4, dbSNP 150 and DGVa structural variants. For both our main database and our GRCh37 database, now have allele frequencies from TOPMed (Trans-Omics for Precision Medicine) and UK10K, and, for pre-existing dbSNP variants, gnomAD. We also have DGVa structural variant updates for Cow, Dog and Mouse.

We have updated phenotype data in Human (NHGRI-EBI GWAS Catalog, OMIM and MIM morbid, ClinVar, Cosmic Gene Census, DDG2P and Orphanet), Mouse (IMPC, MGI), Cat, Chicken, Chimpanzee, Cow, Dog, Horse, Macaque, Pig, Rat (RGD), Sheep, Turkey and Zebrafish (ZFIN).

Microarray probe mapping

Ensembl provide probe mapping for a number of popular commercially-available microarrays, mapping probesets to genomic loci and Ensembl genes. You can get mapping to genes through the transcript pages in the browser and BioMart. We have updated our probe mappings for:

  • Ciona intestinalis
  • Caenorhabditis elegans
  • Chicken
  • Chimpanzee
  • Cow
  • Dog
  • Fruitfly
  • Human
  • Macaque
  • Mouse
  • Mouse strains: 129S1/SvImJ, A/J, AKR/J,  BALB/cJ, C3H/HeJ, C57BL/6NJ, CAST/EiJ, CBA/J, DBA/2J, FVB/NJ, LP/J, NOD/ShiLtJ, NZO/HlLtJ, PWK/PhJ, SPRET/EiJ and WSB/EiJ
  • Pig
  • Platypus
  • Rabbit
  • Rat
  • Saccharomyces cerevisiae
  • Xenopus
  • Zebrafish

Interface updates

You’ll now be able to adjust the y-axis scale of custom wiggle tracks in the browser. We’ll be releasing a blog post about this soon.

File format updates

We’ve updated our sequence ontology terms in our GFF3 files to improve consistency and remove bugs. Read more in this blog post.

Find out more

We’ll be holding a release webinar on Wednesday 6th September at 4pm BST. Register here to learn more about the exciting updates to Ensembl, and ask your questions to the team.

4 thoughts on “Ensembl 90 has been released!

  1. Hello there,

    The symbolic link current_README for the current release is missing from your ftp site.

    I have an automation that fetches http://ftp.ensembl.org/pub/current_README
    to check for new release — but today, it did not find that file.

    That file is very handy for detecting the latest release number — Can you please restore it.

    Thank you for your time

  2. Thanks for letting us know. We missed a job with the release, sorry about that. That’s fixed at our end but will take just over half an hour to appear on the FTP site.