Literature-based gene curation and proposed genetic nomenclature for cryptococcus

Abstract

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 648 Cryptococcus 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 of Cryptococcus gene information, we have collected all published Cryptococcus gene names from the scientific literature and associated them with standard Cryptococcus 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 all Cryptococcus species currently in FungiDB, including Cryptococcus neoformans var. neoformans strains JEC21 and B-3501A, C. neoformans var. grubii strain H99, and Cryptococcus 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 the Cryptococcus research community. The centralization of genomic and literature-based information for Cryptococcus at FungiDB will help researchers communicate about genes of interest, such as those related to virulence, and will further facilitate research on the pathogen.

FIG 1

View of syntenic orthologs on the FungiDB locus summary and Genome Browser page. A view centered on CNAG_06642/TOR1 is shown as an example.

FIG 2

Flowchart for assigning names to Cryptococcus genes. A gene name is assigned based on prior publication in any of the Cryptococcus species or by homology to a gene in the model yeast S. cerevisiae. In cases of ambiguous orthology relationships with many Cryptococcus genes and 1 copy in S. cerevisiae, names are based on the yeast name but with a two-digit number appended. Where there are multiple S. cerevisiae homologs for a C. neoformans gene, the name will be chosen from that which best fits the role or function inferred from the Cryptococcus experiment. Where there are many paralogous copies in both C. neoformans and S. cerevisiae, a unique name not directly tied to the S. cerevisiae name is chosen for the gene.