13.8 million Inter-Homoeologous Variants (IHVs) in wheat called by alignments of the A,B and D component genomes where added as SNP markers

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).

Ensembl Genomes Archive Sites Now Available

Ensembl Genomes now has archive sites for all divisions. These can be found at the following URLs:

http://oct2017-metazoa.ensembl.org

http://oct2017-plants.ensembl.org

http://oct2017-fungi.ensembl.org

http://oct2017-protists.ensembl.org

http://oct2017-bacteria.ensembl.org

The archive sites will allow researchers to access data from old releases via our web-based tools, and additionally will be able to display track hubs containing alignments and features located on older versions of genome assemblies that have since been upgraded in the live site. Archive sites will be searchable and BioMarts will be available where they were produced for the site when live. Schema and API versions for archive sites will be the same as when the data was released, i.e. archive sites will not be updated to use the most recent versions. Ensembl tools will not be active in the initial release, but we are hoping to enable these shortly; likewise, archival REST servers will not initially be available, but will be added in future. Major bugs (i.e. those impeding the usability of the site) will be fixed, but minor bugs will not be.

The first release of the archive sites contains content from release 37. New archive sites will be released at least once a year, under URLs indicating the date of first release of the data they contain. The previously existing archive for Ensembl Plants, http://archive.plants.ensembl.org, will continue to be available at this URL, but also as http://mar2016-plants.ensembl.org, in accordance with the new naming scheme. As previously, data from all recent releases will continue to be available for download at ftp://ftp.ensemblgenomes.org.

posted 2017-11-07

Future releases

Release 38 of Ensembl Genomes is scheduled for 13th December 2017. For more details, see the release intentions.

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 37 (September 2017)

No significant updates have been made for this release.

Release 37 includes a complete re-load of fungal species from the European Nucleotide Archive along with a few species updated manually. Non-coding RNA gene predictions are available for all species, along with updated biomarts and peptide features.

Cross references and protein domain annotations have been updated.

This release of Ensembl Plants adds one of the two recently sequenced Corchorus capsularis (jute) genomes (Nature 2017) and whole genome alignments between the latest Hordeum vulgare (barley) assembly and Oryza sativa (rice), summarised here, and Brachypodium distachyon, summarised here.

​New genomes have been loaded from INSDC, and included in compara. New automatic ncRNA alignments have been added across all protists, using a new algorithm that aims to minimise false positive results by applying taxonomic (and other) filters. Cross references to other resources (such as UniProt and RefSeq) have been updated. Updated phenotypic information from PHI-base 4.3 have been added for phytopathogenic species.

Release notes from previous releases