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Eukaryot Cell. 2014 Jul;13(7):878-83. doi: 10.1128/EC.00083-14. Epub 2014 May 9.

Literature-based gene curation and proposed genetic nomenclature for cryptococcus.

Author information

1
Department of Genetics, Stanford University, Stanford, California, USA.
2
Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA.
3
Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA.
4
Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA jason.stajich@ucr.edu.

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.

PMID:
24813190
PMCID:
PMC4135733
DOI:
10.1128/EC.00083-14
[Indexed for MEDLINE]
Free PMC Article

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