In this project we will provide a manual curation of the literature and gene function for the genomes of the human pathogenic fungus Cryptococcus neoformans and C. gattii. The summary of gene function from published literature, linked it to the genome annotation is a significant result, as it will enable more comprehensive understanding of the biology of the organism as a whole. While genome sequencing of multiple species and years of genetic experiments with Cryptococcus have provided a rich understanding of gene pathways for growth, development, and pathogenesis, the crystallization of this information into curated functions for most genes is lacking. C. neoformans is an effective model genetic system for fungal biology of Basidiomycetes and for investigating mechanisms of pathogenesis so this resource will have importance to a broad collection of researchers. Here we will generate a resource for the community of gene function annotations and linking genes to published literature made freely available through FungiDB, a web-based database with powerful tools for data querying. The two goals of this project are to create a high quality, manual-curated annotation of the function of Cryptococcus genes from the published literature and to make this information easy to search through a website that is connected to sequence information and comparative genomics tools. 1. Literature curation will be performed by an expert curator to associate functions and mutant phenotypes to genes in the 5 sequenced Cryptococcus genomes. Capturing information from published manuscripts will provide clear summary of findings from experiments and associate these functions and cellular roles with specific genes. Similar resources for Saccharomyces and Aspergillus have become essential tools for those research communities. 2. Provide a publically available and searchable website to the curated annotation. The captured knowledge from the manual curation will be deposited into FungiDB to provide researchers with access to data mining and search tools to identify patterns in their data from Cryptococcus genomes. FungiDB provides access to functional or comparative genomics data which will be combined with this new gene annotation information.
This project will develop improved resources and tools for understanding the biology and disease mechanisms of Cryptococcus, a human pathogenic fungus. The resources are the form of gene function curation from the published literature that will improve the speed at which researchers can interpret their results from genetic screens, gene expression profiling. By making this data available in website with tools for data mining and comparative analyses, the project will enable new insights into shared genetic pathways for pathogenesis, growth, development in Cryptococcus and related human pathogenic fungi, which can lead to improved therapeutics targeting these processes.
|Janbon, Guilhem; Ormerod, Kate L; Paulet, Damien et al. (2014) Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet 10:e1004261|
|Inglis, Diane O; Skrzypek, Marek S; Liaw, Edward et al. (2014) Literature-based gene curation and proposed genetic nomenclature for cryptococcus. Eukaryot Cell 13:878-83|