The genome of Melitaea cinxia, the Glanville fritillary butterfly, has fluttered into Ensembl Metazoa. This butterfly has been the subject of a metapopulation study in Finland for over 20 years, and the genome will contribute to a better understanding of the ecological, genetic and evolutionary consequences of habitat fragmentation.

The assembly and gene annotation were produced by the Glanville fritillary butterfly genome project, based at the University of Helsinki.

A new comparative analysis of the A, B and D genomes of hexaploid bread wheat (Triticum aestivum) has allowed us to call orthology relationships between the component genomes, identifying the so called homoeologous genes. Click here for example.

Relationships between the component genomes can now also be browsed in our new region comparison view. Click here for example.

The genomes of 10 new plant pathogen species have been imported, with a wide variety of hosts and spanning the fungi (Capnodiales, Glomerellales, Hypocreales and Pucciniales) and protist (Stramenopiles) divisions.

Three public variation datasets for bread wheat (hosted by CerealsDB) have been added to the Triticum aestivum genome: the 820K Axiom SNP array, the iSelect array, and the KASP probe set.

In total, ~724,000 SNPs have been imported from 248 samples, based on probe alignments to the reference sequence performed at The Genome Analysis Centre (TGAC).

Try out our REST web service, providing language-independent programmatic access to data including sequences, genes and gene trees, and tools including assembly conversion and variant effect predictors. The service now includes for support for finding and working with over 15,000 bacterial genomes.

Future releases

Release 24 of Ensembl Genomes is scheduled for 11th November 2014 - full details can be found here.

posted 2014-08-22
New REST server

The REST server provided by Ensembl Genomes has now been updated to use the latest v3.0.0 codebase provided by Ensembl, plus supplementary endpoints for genome discovery and bacterial family/genome retrieval. For more information on these additional endpoints, please visit:

The new server is available at - please note that will remain accessible until the next release of Ensembl Genomes in October after which point it will be removed.

posted 2014-08-20
New public MySQL server

The Ensembl Genomes public MySQL server is now located on, port 4157. Please update your scripts to use this new location. Note that port 4157 will remain accessible until release 25 of Ensembl Genomes (scheduled for October).

posted 2014-08-19

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 23 (August 2014)

Ensembl Bacteria has been updated to include the latest versions of 15,270 genomes (15,012 bacteria and 258 archaea) from the INSDC archives. Operon and related data from RegulonDB has been loaded for E. coli K12 MG1655

The current release of Ensembl Fungi sees the inclusion of a number of important plant pathogen genomes with a wide variety of hosts from pines to melons, namely Colletotrichum gloeosporioides, Colletotrichum higginsianum, Colletotrichum orbiculare, Dothistroma septosporum, Fusarium fujikuroi, Fusarium pseudograminearum and Puccinia graminis f. sp. tritici Ug99. For the closely related Glomerellale genomes, whole genome alignments are also provided. Data from the latest release of PomBase has been loaded for Schizosaccharomyces pombe, including tracks for transcriptomic data (Marguerat et al. 2012).

Two new species have been added to Ensembl Metazoa: Mnemiopsis leidyi (warty comb jelly), the first ctenophore to be sequenced; and Melitaea cinxia (Glanville fritillary), a butterfly. The assemblies and gene sets have been updated for the European honey bee and the American malaria mosquito, and the purple sea urchin has gained RNA-Seq transcripts. Variation data from VectorBase has been added for Aedes aegypti. Finally, several species had minor updates, such as the addition of mitochondrial chromosomes and ncRNA annotation.

Five new plant genomes have been included in release 23 of Ensembl Plants, ranging from the very small (Ostreococcus lucimarinus a unicellular picoplankton) to the very delicious (Theobroma cacao the cultivated chocolate tree), including two new genomes from the OMAP project, Leersia perrieri (a wild grass) and Oryza rufipogon (brownbeard rice), both added in collaboration with Gramene, and finally, Brassica oleracea (representing the brassica C genome), which complements the existing Brassica rapa (representing the brassica A genome).

A variety of new variation data has been added, including 724,000 variations from 248 samples of Triticum aestivum (bread wheat), new Zea mays (maize) variation data based on Panzea release 2.7 and new Sorghum bicolor (sorghum) variation data from Mace et al. 2013.

Ensembl Protists now includes the genomes of three new plant pathogens from the genus Phytophthora: Phytophthora kernoviae, Phytophthora lateralis and Phytophthora parasitica. Whole genome alignments are now available for all Phytophthora and Pythium species.

Release notes from previous releases