Fungi

Release Intentions

  • New data
    • New load of fungi genomes from ENA
    • New Beauveria bassiana ARSEF 8028 genome
  • Updated data
    • Updated BioMarts
    • Updated protein features
    • Updated peptide pipeline
    • Updated PHI-base 4.3 annotations for ENA imported genomes

Release Notes (Brief)

Release 37 includes a complete re-load of fungal species from the European Nucleotide Archive along with a few species updated manually. Non-coding RNA gene predictions are available for all species, along with updated biomarts and peptide features.

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Ensembl Genomes REST ServiceTo access Ensembl Genomes data from any programming language, try our REST service. For full documentation including examples from a wide range of languages, visit http://rest.ensemblgenomes.org

What's New in Release 37

  • Genomes
    • 811 genomes from 523 species
    • 79 new genomes added, 12 genomes renamed and 395 genomes have updated annotation since release 36
    • New Beauveria bassiana ARSEF 8028 genome
    • Updated annotation for Verticillium dahliae JR2
    • Updated UTR annotation for Fusarium graminearum str PH-1
  • New data
    • ncRNA alignments and gene predictions for all fungal species
  • Updated data
    • Updated BioMarts
    • Updated protein features
    • Updated phenotypic annotation from PHI-base 4.3 for some species

Future Releases

Ensembl Fungi

Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators.

Data access

Data can be visualised through the Ensembl genome browser and accessed programmatically via our Perl and RESTful APIs. Data is also accessible through public MySQL databases and our FTP site containing full data dumps in FASTA, EMBL, GTF, GFF3, JSON and RDF formats

New Ensembl Genomes Archive Sites

Ensembl Genomes now has archive sites for all divisions. These can be found at the following URLs:

http://oct2017-metazoa.ensembl.org

http://oct2017-plants.ensembl.org

http://oct2017-fungi.ensembl.org

http://oct2017-protists.ensembl.org

http://oct2017-bacteria.ensembl.org

The archive sites will allow researchers to access data from old releases via our web-based tools, and additionally will be able to display track hubs containing alignments and features located on older versions of genome assemblies that have since been upgraded in the live site. Archive sites will be searchable and BioMarts will be available where they were produced for the site when live. Schema and API versions for archive sites will be the same as when the data was released, i.e. archive sites will not be updated to use the most recent versions. Ensembl tools will not be active in the initial release, but we are hoping to enable these shortly; likewise, archival REST servers will not initially be available, but will be added in future. Major bugs (i.e. those impeding the usability of the site) will be fixed, but minor bugs will not be.

The first release of the archive sites contains content from release 37. New archive sites will be released at least once a year, under URLs indicating the date of first release of the data they contain.The previously existing archive for Ensembl Plants, http://archive.plants.ensembl.org, will continue to be available at this URL, but also as http://mar2016-plants.ensembl.org, in accordance with the new naming scheme. As previously, data from all recent releases will continue to be available for download at ftp://ftp.ensemblgenomes.org.

PhytoPath

BBSRC Logo

PhytoPath is a joint project between EMBL-EBI and Rothamsted Research, funded by the BBSRC, linking genomic and phenotoypic data of fungal and oomycete plant pathogens.

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.