EMS-type variants from sequenced tetraploid (cv ‘Kronos’) and hexaploid (cv ‘Cadenza’) TILLING populations were added to Ensembl Plants.

Researchers and breeders can search this database online, identify mutations in the different copies of their target gene, and request seeds to study gene function or improve wheat varieties. Seeds can be requested from the UK SeedStor (https://www.seedstor.ac.uk/shopping-cart-tilling.php) or from the US-based Dubcovsky lab (http://dubcovskylab.ucdavis.edu/wheat-tilling).

The Botrytis cinerea genome has been completely re-annotated by the community with the support of Ensembl Genomes. 42 community members (spread across 8 countries) were trained by Ensembl Genomes to use Web Apollo in this re-annotation effort leading to a new gene set comprising of 11,695 manually revised genes (PMID:26913498). This gene set is available on Ensembl Genomes (Botrytis cinerea).

A new assembly of Triticum aestivum cv. Chinese Spring (bread wheat) is now available in Ensembl Plants. The assembly and gene model annotation has been generated by The Earlham Institute, formerly The Centre for Genome Analysis (TGAC). Read more...

The fast protein sequence search of HMMER is now available for all divisions of Ensembl Genomes, via the 'HMMER' link in the menu at the top of every page (e.g. Ensembl Metazoa).

The previous wheat assembly (IWGSC CSS) and every other plant from release 31 is available in the new Ensembl Plants archive site: http://archive.plants.ensembl.org/

New track hubs have been created for more than 900 public RNA-Seq studies, totaling more than 16,000 tracks across 35 plant species (read more).

Please take our user survey!

We're surveying our users to find out more about what you use Ensembl Genomes for, what we do well and what we could do better. The survey should take up only a few minutes of your time, and your answers will be very useful to us: please follow the link to participate https://www.surveymonkey.com/s/HV5T5HZ and feel free to share the link with other users of our service. Thank you!

posted 2015-05-06
Change to BLAST service

From release 27 onwards, the Ensembl Genomes BLAST service uses NCBI Blast+ in place of WUBLAST. Please contact us if you have any questions about this change.

posted 2015-06-16
Change to BioMart mart names

The "virtual" mart names used to identify our live BioMarts will change in release 31 to no longer include the version e.g. protists_mart instead of protists_mart_31. This is to make re-use of URLs etc. easier.

posted 2016-01-11
MySQL database retention policy

As the amount of data in each release of Ensembl Genomes increases, it has become necessary to restrict the number of past releases available on our public MySQL server (mysql-eg-publicsql.ebi.ac.uk).

Shortly before the release 27 of Ensembl Genomes in June 2015, all databases from all releases prior to release 18 will be removed. With each subsequent release, data from the oldest release will be removed at release time, leaving data from the most recent 10 releases only. The removal of each release will be announced with the intentions for the new release approximately 2 months in advance.

Please note that the data available from our FTP site will be unaffected by this change in policy, with data from all releases of Ensembl Genomes remaining available in all supported formats, including full MySQL dumps.

posted 2015-03-25

Register Now for the Wellcome Trust Advanced Course on Fungal Pathogen Genomics.

The course will provide experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis; including genome browsers and comparison tools, data mining using resources such as FungiDB, Ensembl/PhytoPathDB, PomBase, SGD/CGD, MycoCosm, analysis of genome annotation, and next generation sequence analysis and visualization (including RNA sequence analysis and variant calling), and will take place he workshop will be held in Hinxton, UK from 11th-16th May, 2017.
For more information and to apply please follow the link below:

Ensembl Genomes is developed by EMBL-EBI and is powered by Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.

Have a question?

Frequently Asked Questions (FAQs) are now available for all domains of Ensembl Genomes. Have a question? Check if it's been asked before! If there is a FAQ missing, contact us.

What's New in Release 35 (April 2017)

Ensembl Bacteria has been updated to include the latest versions of 44,039 genomes (43,552 bacteria and 494 archaea) from the INSDC archives.

In this release we include an updated gene set for Botrytis cinerea B05.10. This gene set was manually curated by the community using the WebApollo tool. A new strain of Puccinia striiformis was imported from JGI and other new genomes from ENA are also available.

Three species make their Ensembl Metazoa debut: a bdelloid rotifer arrives to represent the Rotifera phylum; the rather attractive (and destructive) Asian long-horned beetle joins our existing Coleoptera (one of which, the red flour beetle, was updated to the latest assembly and gene set in this release); and the Hessian fly, a crop pest, was lured in by all that lovely wheat in Ensembl Plants. The sponge, Amphimedon queenslandica, has also been updated to the latest gene set.

Ortholog metrics were calculated and used to determine a set of "high confidence" orthologs. The metrics included congruence with whole genome alignments and (for closely related species) gene order conservation.

This release of Ensembl Plants includes an updated version of the Sorghum genome and an updated gene build for Zea mays. Additionally EMS variation data has been added for wheat, and QTL data for rice.

This protists release includes new variation data for Phaeodactylum tricornutum generated from 10 ecotypes.

Release notes from previous releases