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

This release of Ensembl Plants includes an updated version of the Hordeum vulgare (barley) genome, the biggest diploid genome yet sequenced, including all new annotation (Nature 2017).

This release of Ensembl Plants includes the latest 1001 variation data set for Arabidopsis thaliana covering more than 10 million variant loci across 1,135 samples (Cell 2016).

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).

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

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.

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What's New in Release 36 (June 2017)

No significant updates have been made for this release. Gene families have been updated to include an additional 142 genomes from release 35.

Gene symbols for 1-to-1 orthologs from Saccharomyces cerevisiae to Botrytis cinerea have been added in this release along with updated BioMarts and PHI-base 4.3 annotations.

RNA gene annotation has been added or updated for 37 metazoan species, 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, and three new sources have been used to annotate protein domains, including MobiDB, a database of intrinsically disordered regions.

This release of Ensembl Plants includes an updated version of the Hordeum vulgare (barley) genome, the biggest diploid genome yet sequenced (Nature 2017). Additionally we have moved to the latest 1001 variation data set for Arabidopsis thaliana covering more than 10 million variant loci across 1,135 samples (Cell 2016). For Triticum aestivum (wheat), 80,829 variation markers from the iSelect 90k array and 13.8 million Inter-Homoeologous Variants (IHVs) have been added. Chloroplast and mitochondrial components (including gene annotations) were imported from ENA.

‚ÄčNew 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 PHI-base 4.3 annotations have been across for phytopathogenic species.

Release notes from previous releases