Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus

Cryptococcus , a major cause of disseminated infections in immunocompromised patients, kills over 600,000 people per year worldwide. Genes involved in the virulence of the meningitis-causing fungus are being characterized at an increasing rate, and to date, at least 648Cryptococcus gene names have been published. However, these data are scattered throughout the literature and are challenging to find. Furthermore, conflicts in locus identification exist, so that named genes have been subsequently published under new names or names associated with one locus have been used for another locus. To avoid these conflicts and to provide a central source ofCryptococcus gene information, we have collected all publishedCryptococcus gene names from the scientific literature and associated them with standardCryptococcus locus identifiers and have incorporated them into FungiDB (www.fungidb.org ). FungiDB is a panfungal genome database that collects gene information and functional data and provides search tools for 61 species of fungi and oomycetes. We applied these published names to a manually curated ortholog set of allCryptococcus species currently in FungiDB, includingCryptococcus neoformans var.neoformans strains JEC21 and B-3501A,C. neoformans var.grubii strain H99, andCryptococcus gattii strains R265 and WM276, and have written brief descriptions of their functions. We also compiled a protocol for gene naming that summarizes guidelines proposed by members of theCryptococcus research community. The centralization of genomic and literature-based information forCryptococcus at FungiDB will help researchers communicate about genes of interest, such as those related to virulence, and will further facilitate research on the pathogen.