Ensembl Genomes

About

The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy.

Metazoa
Protists
Bacteria

: Plants
: Fungi
or browse vertebrate genomes in Ensembl

In each domain, we aim to bring the integrative power of Ensembl tools for comparative analysis, data mining and visualisation across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation.

Releases

What's New in Release 13 (March 2012)

The thirteenth release of Ensembl Genomes features updates to version 66 of the Ensembl software across all divisions, and a number of new genomes bringing the total number of genomes to 341 (full list). Detailed notes can be found here. See the individual homepages for Bacteria, Protists, Fungi, Plants and Metazoa for more information.

Ensembl Bacteria

No significant updates have been made to Ensembl Bacteria.

Ensembl Protists

Release 13 of Ensembl Protists now includes the genome for Toxoplasma gondii ME49. T. gondii is a parasite that can infect warm blooded animals, and causes the disease toxoplasmosis in humans.

Ensembl Fungi

Release 13 of Ensembl Fungi brings in the new species of Magnaporthe oryzae and the two related species Magnaporthe poae and Gaeumannomyces graminis. There is also synteny data for species in the Saccharomycetales and Hypocreales taxonomy groups. The annotation for S. pombe has been updated to reflect the most recent content from PomBase.

Ensembl Plants

This release of Ensembl Plants includes the genome of Brassica rapa, a model organism for several important vegetable and oilseed crops. We have added synteny data for species in the Arabidopsis and Oryza genomes, and the Zea mays genome has been annotated with oligo probes from the GeneChip Maize Genome Array.

Ensembl Metazoa

The 13th release of Ensembl Metazoa includes the genome of Trichinella spiralis, the trichina worm, a nematode parasite of rats, pigs, bears and humans, and responsible for the the disease trichinosis

Future Releases

Release 14 of Ensembl Genomes is scheduled for 22nd May 2012. Detailed notes for this can be found here.

Release notes from previous releases

Working with communities

Ensembl Genomes aims to work with all sections of the scientific community to represent the best annotation for every genome. Our role varies according to the species, and while it may include genome assembly, gene prediction and functional annotation, we are also committed to providing a portal through which genomic data from model organism and community databases can be visualised and analysed in their wider context, and integrated with other data stored in the core repositories maintained by the EBI. The current release of Ensembl Genomes includes databases developed by (or in partnership with) the groups shown on the right:

Collaborate with us

Ensembl Genomes is always looking to engage with new communities. We are highly interested in collaborations that develop resources for genomes in particular areas of interest, and we have a growing range of tools to assist groups with genome sequence to build Ensembl databases and incorporate their data in Ensembl Genomes. If you have data you would like to bring into Ensembl Genomes, mail our helpdesk and we'll be happy to advise you on possible approaches.

Featured content

EMBL-EBI and Rothamsted Research have recently announced the release of the PhytoPath portal, a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. PhytoPath provides access to genomic and phentoypic data from fungal and oomycete plant pathogens, and has enabled a considerable increase in the coverage of phytopathogen genomes in Ensembl Fungi and Ensembl Protists.

PhytoPath contains the genomes of many devastating pathogens, including Phytophthora infestans, which brought on the Irish potato famine of the mid-19th Century and has re-emerged as an important biotic threat to global food security. Also included are the genomes of several cereal fungal pathogens that regularly lower global grain production by between 15 and 30%: Magnaporthe oryzae (rice and wheat blast), Puccinia graminis and P. triticina (the rusts), the wheat leaf-infecting pathogen Septoria tricitici (Mycosphaerella graminicola) and Fusarium graminearum (Gibberella zeae), a fungus which produces mycotoxins that are harmful to human and animal health.

PhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes.

PhytoPath is funded by the BBSRC.

Ensembl Genomes is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute