Announcing FungiDB 2.1 release

On behalf of the FungiDB development team I am pleased to announce the release of FungiDB 2.1 which includes 39 Fungal genomes from Ascomycota, Basidiomycota, and Mucormycotina (Zygomycota) and 6 genomes of Oomycetes.  This release builds on the 2.0 release from August to include 6 additional species, RNA-Seq from a population of Neurospora strains, growth time points in 3 fungi Coprinopsis, Neurospora, and Rhizopus, and Phytophthora species. The 6 new genomes include Batrachochytrium dendrobatidisCoprinopsis cinereusHistoplasma capsulatumCoccidioides posadasii, Rhizopus delemar (formerly oryzae), and Ustilago maydis.

While the Oomycetes are not true Fungi, as phylogenetically they are in a very distinctly different clade, however we have included them in the database as part of collaboration with Brett Tyler. It may be that some aspects of the convergent evolutionary patterns among these groups can be revealed by having the data in a common system and use of the same tools.

Several human pathogenic and opportunistic fungi are now available in the system including 2 strains of Histoplasma capsulatum and 2 species of Coccidioides, Candida albicans, 2 Cryptococcus gattii strains, C. neoformans var grubii, and 2 C. neoformans var neoformans strains, Fusarium oxysporumAspergillus fumigatus and A. terreus. With the homolog tools available in the FungiDB system, one can map functional data from onto genes in these fungi from related models in the filamentous or yeast species.

Plant pathogens Magnaporthe grisea, Ustilago maydis, Puccinia graminis, and several Fusarium species, and the collection of 6 Oomycetes also provide a platform for comparative genomics among plant pathogens.

Functional annotation data have been imported from model system databases for Aspergillus nidulans, Saccharomyces cerevisiae, and C. albicans.  We also generate predicted GO annotations from InterPro based analyses.

The development team at UC Riverside including Raghu Ramamurthy, past member Daniel Borcherding, and new member Edward Liaw; our collaborators on Oomycete data at Oregon State Brett Tyler and Sucheta Tripathy; and the EuPathDB developers and systems teams that have been essential partners in everything from assisting in data development and software debugging to database administration and web and systems administration.

Future work

Work is likely to begin in the next quarter to curate and support further literature based annotation of gene function in the Cryptococcus species. In addition we plan to expand the supported phenotypic data for Neurospora to support work from the Program Project grant and the phenotyping of the systematic gene deletion collection.

Additional support will be rolled out for more functional and evolutionary genomics data including expanded RNA-Seq datasets, population genetic data sets for several species with cohorts of sequencing of strain populations. We plan to continue to add additional species, with priorities focused on pathogens and model systems, but are interested in the community feedback of specific species that are must include targets in future releases. Please email help[AT]fungidb.org with your suggestions or fill out feedback on the “Contact Us” link on the FungiDB page.

Support
The work in this release was supported by grants from the Burroughs Wellcome Fund and the Alfred P. Sloan Foundation.The Oregon State team is supported by grants from the Agricultural and Food Research Initiative of the  USDA National Institute for Food and Agriculture.  The EuPathDB team is supported by grants from the NIH, Gates Foundation, and Wellcome Trust. Without the direct and indirect support of these funders none of this would have been possible.  All web and computational resources for FungiDB are currently housed at the Univ of Pennsylvania or the University of Georgia, thanks to the many system administrators who keep these services running that have allowed us to make this release.