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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.

What's New in Release 35

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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

New manually-curated gene set for Botrytis cinerea

The Botrytis cinerea genome has been completely re-annotated by the community with the support of Ensembl Genomes. 42 community members (spread across 8 countries) were trained by Ensembl Genomes to use Web Apollo in this re-annotation effort leading to a new gene set comprising of 11,695 manually revised genes (PMID:26913498). See Botrytis cinerea

  • Genomes
    • 735 genomes from 444 species
    • 104 new genomes and 26 updated genomes from INSDC
    • New genome from Puccinia striiformis f. sp. tritici PST-130 imported from JGI
    • Updated Botrytis cinerea genome with community-based annotations
  • Data
    • Updated phenotypic annotation from PHI-base
    • Updated protein features and GO annotations
    • Updated peptide comparative and pan-taxonomic genomics
    • GO term projection from S. cerevisiae and S. pombe to orthologues in other species

Ensembl Fungi

Ensembl Fungi is a genome browser for fungal genomes. A majority of these genoms 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.