When many of us think about fungi, we tend to think of decay and disease. There are, of course, many pathogenic fungi that have a significant impact on human, animal and plant health. However, fungi are also the unsung heroes in many aspects of our life, including food production and other important breakthroughs in medicine and household products (such as detergents).
Release 105 of Ensembl Fungi has 1506 genomes, spanning across many fungal families. Of these, 477 are new assemblies and gene sets that we have imported from the European Nucleotide Archive across the following phyla: Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, Microsporidia, Glomeromycota, Ascomycota and Basidiomycota. The new data encompass a wide range of fungi: from pathogens such as Synchytrium endobioticum that cause potato wart disease (or black scab) and Zopfia rhizophila that cause Zopfia root rot in asparagus to Friedmanniomyces endolithicus, resistant to acute doses of gamma radiation, to the wine spoilage yeast Brettanomyces bruxellensis.
Fifteen genomes have also been imported from VEuPathDB in an attempt to better align the fungal data sets represented in FungiDB and Ensembl Fungi. These fifteen were chosen carefully to capture data that Ensembl Fungi did not have already, and more will be incorporated in future releases.
All the genomes in Ensembl Fungi have been annotated with Rfam alignments (Rfam version 14.2), protein features through InterProScan and pathogen-host interaction phenotypes from PHI-base. Our BioMarts have been updated too, and gaps that were identified by our users have now been filled. For instance, many Candida species are now available through BioMart.
We rely on the NCBI taxonomy for our species classifications. Unsurprisingly, there are always many changes to the fungal taxonomy each time we do a major update to Ensembl Fungi. Fortunately, you can type in the taxonomy ID into our search box to locate the right genome or refer to the list of renamed genomes via our FTP page. Please also remember to check any URLs that you may have bookmarked.
We have also recomputed our fungal gene trees using 375 fungal species. As there have been significant improvements to the Ensembl Compara algorithms under the hood and a reduction in the number of fungal species represented when compared to the previous fungal Compara, changes in the gene trees are to be anticipated.