FungiDB: an integrated functional genomics database for fungi

Abstract

FungiDB (http://FungiDB.org) is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center (http://EuPathDB.org). FungiDB uses the same infrastructure and user interface as EuPathDB, which allows for sophisticated and integrated searches to be performed using an intuitive graphical system. The current release of FungiDB contains genome sequence and annotation from 18 species spanning several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. Additionally, FungiDB contains cell cycle microarray data, hyphal growth RNA-sequence data and yeast two hybrid interaction data. The underlying genomic sequence and annotation combined with functional data, additional data from the FungiDB standard analysis pipeline and the ability to leverage orthology provides a powerful resource for in silico experimentation.

Figure 1.

Screen shot of the FungiDB home page. (A) The banner section present on all FungiDB webpages provides links to registration, login, and contact us forms, ID and text searches, information and help, and all available searches and tools. (B) The side bar provides expandable tabs with information such as a data summary table, community events, news, tutorials and help links. (C) The central portion of the home page contains three sections, the left column contains searches that return genes, the middle column contains searches that return other entities such as genomic sequence, ESTs, DNA motifs and the third (right column) section contains tools such as BLAST, sequence retrieval and web services. The plus symbols can be expanded to reveal specific searches (upward pointing red arrow). Green insert is an example search page following selection of a ‘genes by species’ search.

Figure 2.

(A) Screen shot of a search strategy with the first step being the results of running the search shown in Figure 1C (inset). Engaging the ‘Add Step’ button reveals a popup with all available searches in FungiDB. Set operations (intersect, union and minus) are used to combine searches with each other in a search strategy (green box). (B) The filter table appears below the search strategy and shows results across all species in FungiDB. Selecting any of the cells will filter the results and show them in the results table shown in C. (C) The results of any search are displayed in a dynamic table that allows removing (click on the ‘x’ next to the column name), adding (green box) and moving (drag and drop) columns, downloading results and adding results to the basket (red upward pointing arrow). (D) Selecting any of the record IDs in the first column opens a record page (the gene page is shown in D). The gene page includes sections including the gene ID and gene product name, genomic context showing synteny with related species in FungiDB, annotation with links to the ‘User Comment’ form (shown in E), protein information (i.e. interpro domains, hydropathy plots, signal peptide prediction, etc.), expression data (where available) and the sequence. (E) The user comment form allows comments by the community including free text, PubMed IDs, GenBank accession numbers, attaching images and files, and linking comments to multiple records. (F) A genome browser view in FungiDB accessible from the genomic context view in the gene page or the tools section. Tracks can be loaded in the genome browser such as synteny as shown in F and RNA sequence coverage plots as seen in (G).

Figure 3.

Screen shot of a multi-step search strategy in FungiDB. (A) The main body of the search strategy—Step 1 asks for all genes in FungiDB annotated with an EC number, Step 2 uses a union operation to combine results from Step 1 with all genes with ‘metabolic process’ genome ontology association, Step 3 transforms the results from Step 2 into their orthologs in all species in FungiDB, Step 4 intersects results from Step 3 with a substrategy (B), Step 5 intersects the results of Step 4 with results from an orthology phylogenetic pattern search that asks for all genes in FungiDB that do not have orthologs in mammals. A filter is applied (see Figure 2B) to the results in Step 5 to reveal only C. neoformans genes. (B) An expanded view of the substrategy that was combined with Step 3 in A, which defines all orthologs of genes in R. oryzae that are upregulated in hyphae based on RNA sequence data. Saved strategies may be shared with others using a unique strategy URL shown in the inset (http://fungidb.org/fungidb/im.do?s=c485b8fe6e1769bd).