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

PhytoPath

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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. For information on how to cite Ensembl Genomes click here.

Register now for the EBI training course in Plant and Pathogen Bioinformatics 13th-15th November 2017, Hinxton, UK

This course will provide an introduction to data resources, tools and essential bioinformatic techniques for biologists studying plants and their pathogens. It will be delivered using a mixture of lectures, practical computer sessions and include discussions based on relevant case studies and public domain data. For more details, go to http://www.ebi.ac.uk/training/events/2017/plant-and-pathogen-bioinformatics-0.

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.

Citing Ensembl Genomes

If you've used Ensembl Genomes in your work, please cite the most recent overview article below and the Ensembl Genomes release you retrieved your data from. References for the specific genome assembly can be found on the ‘More information and statistics’ page for each species (e.g., Saccharomyces cerevisiae).

Kersey PJ, et al. Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res. 2016 Jan;44(D1) D574-80. doi:10.1093/nar/gkv1209. PMID: 26578574; PMCID: PMC4702859.