We are pleased to announce the release of Ensembl 110, and the corresponding release of Ensembl Genomes 57. This release brings exciting updates, such as the addition of regulation data to five animal genomes studied extensively in agriculture, the re-annotation of genomes in Ensembl Bacteria, and changes to REST API endpoints in our comparative genomics data. We have updated genomes across the different Ensembl sites, the addition of 15 rice varieties and invertebrate metazoan genome assemblies.

Can’t find a species you are looking for? Don’t forget that new genome assemblies and annotations are continuously added to Ensembl Rapid Release.

Vertebrates

A major update in Ensembl is the addition of new regulation data. We have collaborated with the GENE-SWitCH and AQUA-FAANG consortia to add regulatory annotation in Pig, Chicken, Atlantic salmon, Turbot and European seabass. You can now visualise and find open chromatin regions and promoters in these species in the genome browser.

A screenshot of the ESRRB region in Gallus gallus in the Ensembl Location tab. You can now visualise promoter and open chromatin regions in the Regulatory Build track. Credit: Ensembl.

Three new plugins for the Ensembl Variant Effect Predictor (VEP) are now available:

We have also extended the analysis options available for structural variants (SV) in Ensembl VEP including more detailed molecular consequence predictions, more efficient integration of information from reference SV sets and support for breakend variant annotation and the integration of CADD-SV scores.

A release wouldn’t be complete without updates in human. We’re excited to tell you that the human genome assembly has been updated to the latest patch release GRCh38.p14. Note, however, that genes on patches will only appear on scaffold coordinates. Further, in the GFF3 annotation files, you will now find that MANE and Ensembl canonical attributes have been added as tags. Y pseudoautosomal region (PAR) genes are now stand-alone genes and are no longer taken from X, but MANE attributes remain on X PAR genes only.

Updated genomes

New Rattus norvegicus (Norway rat) strains

Bacteria

This release brings an extensive update to Ensembl Bacteria. We introduce, for the first time, in-house gene annotation across bacterial genomes, through a collaboration between the Microbiome Informatics and Ensembl microbial groups at the EBI.  Consistent annotation allows for better comparisons of prokaryotic species and pangenomes, and closer harmonisation with MGnify MAG (metagenomic assembled genomes) catalogues. Furthermore, the robust set of pipelines developed in this process allow Ensembl to address outdated and unannotated data sets in the prokaryotic space easily. You can read more about this in an upcoming Ensembl blog. Additionally, we used this chance to put Global Alliance for Genomics and Health (GA4GH) guidelines for systematic gene naming in place for the bacterial genes.

We are transitioning gradually to the new annotation in Ensembl Bacteria. We have updated annotations for all species in Ensembl Bacteria with the exception of 115 genomes, which represent widely cited community annotations or are model organisms. These 115 species, which are part of Ensembl’s pan-taxonomic comparative study, will not change for the foreseeable future, but now include AlphaFold predictions for proteins.

A screenshot of the AlphaFold prediction of the infA-1 transcript in Escherichia coli str. K-12 substr. MG1655. Credit: Ensembl.

Plants

The new release includes a number of interesting additions to Ensembl Plants. For all wheat enthusiasts, we have added the Triticum aestivum IWGSC RefSeq v2.1, as well as the T. aestivum cv. Renan (GCA_937894285.1) assemblies to our database. You can find both genomes in the T. aestivum List of Cultivars. We have also updated Eragrostis tef (Teff) GCA_024500355.1 and Populus trichocarpa (Black cottonwood) GCA_000002775.4.

For rice, we have updated to the latest Oryza sativa (Rice) GCA_001433935.1 gene set and have added a whopping 15 cultivars! You can find all new cultivars in the O. sativa List of Cultivars (see screenshot below). These include:

A screenshot of the Oryza sativa Japonica species information page. All newly added cultivars are available under the link View list of cultivars. Credit: Ensembl.

Metazoa

Gene trees within Ensembl Metazoa have been expanded to cover 275 species by dividing them into 3 taxonomic clade sets: Metazoa, Protostomia, and Insecta. In addition, the release and update frequency of metazoan gene trees will change, with Metazoa and Protostomia being updated in every even-numbered release and Insecta being updated in every odd-numbered release. You can read more about this in an upcoming Ensembl blog. 

You will also find updates in the following genomes:

We have also added the following genome assemblies for existing species:

The invertebrate metazoa community have been busy releasing new genome assemblies, therefore, you can now find the following species in Ensembl:

Other updates and highlights

This blog post was originally published on the Ensembl blog.

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