The Ensembl Genomes project has celebrated its 4th year anniversary in the beginning of this week and now we are pleased to announce another milestone: Ensembl Genomes release 18.

In our latest release, we provide several new species for all divisions of Ensembl Genomes, which includes three new genomes in Ensembl Fungi (Yarrowia lipolytica, Cryptococcus neoformans and Trichoderma reesei); one new genome in Ensembl Protists (Guillardia theta); four new genomes in Ensembl Metazoa (Brugia malayi, Loa loa, Megaselia scalaris and Strigamia maritima); one new species in Ensembl Plants (Medicago truncatula). We have also incorporated the latest versions of prokaryotic genomes from INSDC in Ensembl Bacteria.

NOTE: The public mysql database will be available on Monday, April 29th 2013.

The detailed features of this new release are:

* Bacteria

• Addition of cross-references to Rhea in Ensembl Bacteria;
  
• New and updated genomes: 6,305 bacterial genomes in total, all deposited in ENA.

* Fungi

• Three new species are included in Ensembl Fungi: the human pathogen Cryptococcus neoformans, and the industrially important species Yarrowia lipolytica and Trichoderma reesei;
• New Botryotinia fuckeliana assembly and EST data;
• Updated annotation for Schizosaccharomyces pombe from PomBase.

* Protists

• Extended taxonomic coverage with the newly added Guillardia theta genome;
• Updated DNA alignments and synteny for tramenopiles genomes.

* Metazoa

• Two new parasitic nematode genomes: Brugia malayi (causative agent of lymphatic filariasis) and Loa loa (causative agent of subcutaneous filariasis);
• The genomes of scuttle fly (Megaselia scalaris) and the centipede Strigamia maritima are now available. The latter is the first myriapod genome to be included in Ensembl Metazoa;
• Updated assembly for Caenorhabditis elegans and Schistosoma mansoni.

* Plants

• Barrel clover (Medicago truncatula) is now available. This is the second legume genome to be included in Ensembl Plants;
• New visualization of barley (Hordeum vulgare) physical map anchoring the gene space assembly;
  
• Whole genome alignments between barley, rice and brachypodium;
• Updated maize (Zea mays) assembly to version 3;
• New variation datasets for barley and Brachypodium distachyon;
• Alignments of Triticum aestivum (bread wheat) WGS, TSA and EST assemblies against the barley genome are now available. The bread wheat data can also still be visualised in the context of Bracypodium distachyon;
• Protein domain predictions and cross references have been updated for most plant genomes;
• New pairwise alignments between several genome sequences.

* Software migration to Ensembl 71

Have fun!

The Ensembl Genomes Team

The Ensembl Genomes project is pleased to announce release 17 of Ensembl Genomes.

Our latest release brings over 6,000 bacterial genomes into Ensembl for the first time ever!  Users can browse these data interactively on the web with our graphical interface. Programmatic access is available through the Perl and RESTful Ensembl APIs, and through publicly accessible mysql databases. Full data dumps such as DNA sequence and protein sequence in FASTA format, annotations in GTF format, and mysql dump files are also provided on our FTP sites.

Due to this sheer number of new genomes in Ensembl Bacteria in release 17, BioMart access is no longer possible and we are now working on alternative and more powerful data retrieval tools.

An increased number of bacteria (over 120 genomes) has now been used for comparative genomics analyses across a wider range of non-bacterial genomes (from both Ensembl and Ensembl Genomes projects). This is known as Pan-taxonomic Compara and can be visualised in the gene views on the browser or accessed through the Compara database.

In addition to the thousands of new bacterial genomes, we also have six new genomes in Ensembl Fungi and one new genome in Ensembl Protists. We have also improved existing genomes and added new variation, comparative genomics and transcriptomics data for several species.

The significant milestones of this release are:

• Ensembl Bacteria:

* Protein families are now classified based on PANTHER and HAMAP matches. Gene trees are provided for several but not for all bacterial genomes

* Pan–taxonomic compara now contains 123 key bacterial genomes

* Gene families are now populated by dividing all proteins on all genomes by HAMAP and PANTHER classification provided by InterPro

• Ensembl Fungi:

* Six new genomes: Komagataella pastoris, Sporisorium reilianum, Pyrenophora teres, Pyrenophora tritici-repentis, Glomerella graminicola and Melampsora larici-populina

* New EST alignments for Melampsora larici-populina, Glomerella graminicola and Leptosphaeria maculans

* Mycosphaerella graminicola has been renamed to Zymoseptoria tritici

• Ensembl Metazoa:

* Updated gene sets for Anopheles gambiae

* Updated gene sets for Drosophila pseudoobscura (FlyBase version 2.30) and Drosophila simulans (FlyBase version 1.4)

* Updated cross-references for all 12 drosophilid species

* A missing chromosome in beetle (Tribolium castaneum) was also reinstated, and its gene models updated

• Ensembl Plants:

* New and extensive variation dataset for Hordeum vulgare (barley)

* Triticum aestivum (wheat) EST and RNA-seq alignments in the syntenic context of Brachypodium are now available

* New wheat sequence search facility based on extensive genomic and transcriptomic data aligned to Brachypodium

* Solanum tuberosum (potato) EST and RNA-seq alignments are also now available

* New pairwise alignments between several plant genomes.

• Ensembl Protists:

* A new genome of a flagellated protozoan parasite, Giardia lamblia, is now available

• Software migration to Ensembl 70

Have fun!

The Ensembl Genomes Team

The Ensembl Genomes Project is pleased to announce release 16 of Ensembl Genomes.

In this release, new species include Hordeum vulgare (barley), Solanum tuberosum (potato) and Musa acuminata (banana) in Ensembl Plants; and Nasonia vitripennis (the jewel wasp) and Anopheles darlingi (Central and South American malaria mosquito) in Ensembl Metazoa. Improvements on the wheat assembly and the ability to highlight annotations in gene trees have also been released.

Barley is among the world’s earliest domesticated crop species, is the fourth most abundant cereal worldwide and is a traditional model for plant genetic research. It has a large diploid genome of about 5.1Gb in size. A draft genome sequence containing the majority of barley genes and integrated with the physical map has been recently published in Nature. The genome is now available in Ensembl Plants.

We have improved the alignment of a draft wheat assembly to Brachypodium distachyon and updated our presentation of wheat homoeologous SNPs using the Brachypodium reference.

Significant milestones of this release are:

* Ensembl Genomes displays the inferred evolutionary history of gene families in gene trees. Branches sharing specific annotation terms can now be highlighted indicating the evolution of gene function (view example) .

* Ensembl Plants updates:

• Three new genomes: Hordeum vulgare (barley), Solanum tuberosum (potato) and Musa acuminata (banana)
• New EST alignments for Physcomitrella patens (moss)
• New repeats feature annotation for Selaginella moellendorffii (lycopod)
• Updated gene models for Glycine max (soybean)
• Updated peptide comparative genomics

* Ensembl Metazoa updates:

• Two new species: Nasonia vitripennis (the jewel wasp) and Anopheles darlingi (Central and South American malaria mosquito),
• New variation dataset for Anopheles gambiae (from the insecticide resistance study at the Liverpool School of Tropical Medicine) and use of LD and transcript displays for A. gambiae variation data,
• Updated Pristionchus pacificus cross-references,
• Updated Caenorhabditis brenneri, Caenorhabditis japonica and Caenorhabditis remanei gene models and assembly,
• Update Drosophila melanogaster to FlyBase 5.46 including the gene models and variation consequences.

* Ensembl Fungi updates:

• Addition of Fusarium oxysporum variation database based on sequencing of 27 different strains from the ENA Sequence Read Archive,
• Updated data in Puccinia graminis,
• Descriptions and gene names were imported from the Broad Institute,
• Missing InterPro annotations were added,
• ncRNA stable identifiers were updated,
• repeat features to Botryotinia fuckeliana.

* Ensembl Protists updates:

• repeat features added for Albugo laibachii,
• protein features updated for all species.

* Update of pan homology comparative genomics database to include latest versions of genomes from Ensembl and Ensembl Genomes

* Updated BioMarts

* Software migration to Ensembl 69

The Ensembl Genomes Team

Dear all,

The Ensembl Genomes Project is pleased to announce release 15 of Ensembl Genomes.

This release contains two new genomes, bringing the total genomes supported to 354. Main highlights are:

* Two new species in Ensembl Fungi:  Leptosphaeria maculans and Trichoderma virens. New variation dataset is available for Puccinia graminis.

* Cross-references to other databases have been updated for Ensembl Metazoa.

* A set of homoeologous SNPs between wheat A, B and D genomes using wheat contigs aligned to Brachypodium distachyon as a reference framework is now available, a structural variation dataset for Sorghum bicolor has been imported from dGVA, and a variety of small improvements to our assembly, annotation and variation datasets have been incorporated. See the Ensembl Plants homepage for details.

* RNA-Seq data  from the ENA Sequence Read Archive have been aligned to the genomes of Pythium ultimum, Phytophthora sojae and Albugo laibachii. A variation database for Phytophthora infestans using  ENA Sequence Read Archive of three different strains is now available.

* Software migration to Ensembl 68

* New 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 you would like to see, contact us.

The Ensembl Genomes Team

The Ensembl Genomes Project is pleased to announce release 14 of Ensembl Genomes.

This release contains 11 new genomes, bringing the total genomes supported to 352. Main highlights are:

* Four new genomes in Ensembl Protists: the ciliate protozoa Tetrahymena thermophila; two oomycetes pathogens of the model plant Arabidopsis thaliana, Hyaloperonospora arabidopsidis and Albugo laibachii; and Entamoeba histolytica, a parasitic protozoan that infects primates, including humans.

* The addition of tomato (Solanum lycopersicum), foxtail millet (Setaria italica), and a disease resistant rice (Oryza brachyantha) to Ensembl Plants. Tomato has now been added to the pan-taxonomic comparative analysis, and synteny data is available for the Oryza genomes. Two new variation datasets covering the Maize HapMap 2 project and African rice (Oryza glaberrima) are now available.

* Two new species, Monarch butterly (Danaus plexippus) and the Postman butterfly (Heliconius melpomene), have been added to Ensembl Metazoa. Updated gene sets are now available for Aedes aegypti, Culex quinquefasciatus, Ixodes scapularis and Caenorhabditis elegans. The underlying genome assembly for Caenorhabditis briggsae has been updated, and a new gene set is provided. Whole genome DNA alignments (LASTZ and translated BLAT) have been prepared between C. elegans and the six other nematodes.

* Two new species in Ensembl Fungi: Sclerotinia sclerotorium and Botryotinia fuckeliana. Projection of manual GO (Gene Ontology) annotation from S. pombe and S. cerevisiae to other species based on protein homology is now available.

* Software migration to Ensembl 67

The Ensembl Genomes Team

The Ensembl Genomes Project is pleased to announce release 13 of Ensembl Genomes.

This release contains 6 new genomes, bringing the total genomes supported to 341. Main highlights are:

* Software migration to Ensembl 66

* The addition of Brassica rapa to Ensembl Plants, as well as synteny data for species in the Arabidopsis and Oryza genomes and new oligo probe mapping from the GeneChip Maize Genome Array for Zea mays

* A new species (Toxoplasma gondii ME49) added to Ensembl Protists and the genome of Trichinella spiralis is now available in Ensembl Metazoa.

* Three new genomes in Ensembl Fungi: Magnaporthe oryzae, Magnaporthe poae and Gaeumannomyces graminis. There is also synteny data for species in the Saccharomycetales and Hypocrealestaxonomy groups. The annotation for S. pombe has been updated to reflect the most recent content from PomBase.

* 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.  Genomes of pathogenic organisms from this project including the causative agents of diseases such as potato blight, rice blast and wheat rust can be found in this release of Ensembl Genomes.

The Ensembl Genomes Team