[ensembl-announce] Ensembl Genomes release announcement

[denise at ebi.ac.uk]

Dear all,

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