Fungi

Release Intentions

  • No significant updates planned for this release

Release Notes (Brief)

No significant updates have been made for this release.

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What's New in Release 34

No significant updates have been made for this release.

Future Releases

Wheat Stem Rust Genomes

Wheat stem rust caused by Puccinia graminis f. sp. tritici is one of the most damaging diseases of wheat, It can cause more than 70% reduction of yield within weeks of infection. In spite of its the high mobility of its wind-borne spores, the wheat stem rust disease has largely been under control for over the past three decades, owing to the use of resistant wheat cultivars. However, in 1999, a new virulent race (TTKSK ) was identified in the wheat fields of Uganda, known as Ug99. Ug99 isolate has a unique virulence profile, and that can over come many key wheat rust resistance genes, including gene Sr31. Rust pathogens change rapidly, often by mutation, resulting in six additional variants are now recognized in the Ug99 lineage (demonstrating the rapid evolutionary change that typifies pathogen genomes). All exhibit differ in virulence patterns and hence wheat with important resistance genes like Sr24 and Sr36 are also now susceptible to these variants of Ug99. By 2007, Ug99 had spread via wind movements out of East Africa, into Middle East and is on the verge of spreading into Europe and Asia. Ug99 and its variants are considered a major threat to wheat production with an estimated 80-90% of global wheat cultivars susceptible. The genome sequences of Ug99 and the wheat genome should help in the identification and characterisation of stem rust virulence genes, and of wheat genes capable of conferring durable resistance to it. The Ug99 genome is now made available in Ensembl Genomes, in collaboration with BROAD Institute and funded by The Bill and Melinda Gates Foundation.

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.

Register Now for the Wellcome Trust Advanced Course on Fungal Pathogen Genomics

The course will provide experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis; including genome browsers and comparison tools, data mining using resources such as FungiDB, Ensembl/PhytoPathDB, PomBase,SGD/CGD, MycoCosm, analysis of genome annotation, and next generation sequence analysis and visualization (including RNA sequence analysis and variant calling), and will take place he workshop will be held in Hinxton, UK from 11th-16th May, 2017.
For more information and to apply please follow the link below:

26 new genomes now available in Ensembl Fungi

From release 28 forward, all fungal genomes whose sequence and annotation has been completed and submitted to the the International Nucleotide Sequence Database Collaboration (i.e. the ENA, GenBank and DDBJ databases) is available in Ensembl Fungi. The release now consists of a total of 589 genomes, of which 536 have been taken from the archives and 53 taken directly from other sources. The new genomes have been functionally annotated with InterPro entries and GO terms using InterProScan v55, and manually curated GO terms have been projected from Saccharomyces cerevisiae and Schizosaccharomyces pombe to 1:1 orthologues in other species.

The Fungal Compara is now calculated across 339 species. This includes all previously included genomes and the new imports, selected to ensure each species is represented by at least one genome. Representative sequences have been selected by date of submission to the INSDC (the earliest sequences submitted have been preferentially included).

Note: The new genomes are not currently available through BioMart - this will be addressed in a future release. New genomes are also stored in MySQL collection databases, which may require changes to data access in some cases.

PhytoPath

EMBL-EBI and Rothamsted Research have jointly released the PhytoPath portal, a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. PhytoPath provides access to genomic and phentoypic data from fungal and oomycete plant pathogens, and has enabled a considerable increase in the coverage of phytopathogen genomes in Ensembl Fungi and Ensembl Protists.

PhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes.

BBSRC Logo PhytoPath is funded by the BBSRC.