Resources For Genomes and Polymophism For Wheat Stem Rust In Ensembl Fungi

The Ensembl genome analysis software suite is a powerful range of tools for the storage, analysis, and visualisation of genomic scale data. As part of the Ensembl Fungi project, we have incorporated data from the wheat stem rust pathogen (http://fungi.ensembl.org/Puccinia_graminis) into the system. Data access is provided via a range of user interfaces, including an interactive genome browser, two programmatic APIs (one using Perl, the other using REST), a public mysql database, an FTP site, and a further selection of interfaces to query-optimised gene- and variation centric data warehouses constructed using the BioMart tool. A particularly powerful feature of the web interface are a range of displays for looking at variation data, including gene-centric displays, linkage disequilibirum, links between variants and populations, associations with reported phenotypes etc.; some of these views are already activiated for P. graminis. Data currently included for P. graminis include the genome sequence and annotation for the reference 7a strain, as well as variant calls made by the Broad Institute from a variety of 7a races and additionally from a 4a x 7a mapping population developed at the Cereal Disease Laboratory of the USDA-ARS; we are currently in collaboration with both groups to develop sequence and tools for Ug99, and intend to construct a comprehensive catalogue of wheat stem rust variation as the data from more strains and races becomes available. Ensembl Fungi additionally contains the genome sequence of the wheat yellow rust, Puccinia triticina, as well as 25 other fungi. All genomes are fed through a comparative analysis pipeline with each release, and are additionally functionally annotated using InterPro. Many common fungal families are not represented in the current annotation set; and that an unusually low percentage of genes (compared with other sequenced genomes) have been functionally classified. This reflects the repetitive nature of the P. graminis genome and the heterokaryotic nature of the species, both of which make the production of contiguous assemblies a challenge with existing sequence technologies. The Ensembl Compara visualisation provides one route to identify genes probably split over fragmented assemblies. We are developing a system to allow the projection of features (gene and variant calls) between successive versions of anassembly, so that data is not lost as assemblies improve over time, which may prove especially important for P. graminis.