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.

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

“…The Convention on Biological Diversity mandates that every country develop an ex situ microbial germplasm repository and the formalisation of these public resources should increase the access to well-characterised microbial resources (Secretariat 1992). Because much genetic research with fungal model systems has evolved into genomics research, shared data resources such as the JGI MycoCOSM system (Grigoriev et al 2013) and fungiDB (Stajich et al 2012) are increasingly important. As more fungi, beyond model systems, enter the big data realm, other online resources, such as the JGI Knowledge Base (Palumbo et al 2014), will become more important for fungal genetics.…”

“…Other data resources for A. nidulans include a curated gene compendium (http://www.fgsc.net/Aspergillus/gene_list/index.html) and annual bibliography (http://www.fgsc.net/scripts/biblioNEW.asp) as well as collaborative genome tools, including a central data repository (Mabey et al 2004) and also the Aspergillus Genome Database (Arnaud et al 2012). With a general move away from organism-specific database resources, the A. nidulans community has migrated to the fungiDB integrated genomics database for fungi (Stajich et al 2012). …”

“…The initial genome analysis was fundamentally comparative, and the Broad online data resources emphasised this comparative aspect, although like other fungal genome resources the Broad Aspergillus site is now only available as an online archive (http://archive.broadinstitute.org/ftp/pub/annotation/fungi/aspergillus/). Other shared genome resources for Aspergillus include the Aspergillus site (http://www.aspergillus.org.uk/) as well as increasing amounts of content at fungiDB (Stajich et al 2012). The NCBI Short Read Archive includes over 1600 projects using Aspergillus including transcriptome and genome sequences of diverse species as well as multiple projects with the reference genome strain FGSC A4 (Pontecorvo et al 1953b).…”

Detection of the oomycete Pythium insidiosum by real-time PCR targeting the gene coding for exo-1,3-β-glucanase

“…Beacon Designer software version 3.0 (Premier Biosoft) was used to design the primers Pr77 (59-AAGACGTACTACTGGAAG-39)/Pr78 (59-CATAAAGTCGAGCCAGAA-39) for RT-PCR amplification of the reference PinsEXO1 gene (GenBank accession number GU994093). The primers were searched using BLAST against a draft genome sequence of P. insidiosum (Rujirawat et al, 2015) and genomes of six other Pythium species (Pythium aphanidermatum, Pythium arrhenomanes, Pythium irregular, Pythium iwayamai, Pythium ultimum and Pythium vexans) deposited in the FungiDB database (Stajich et al, 2012) for off-target priming (date performed: 22 May 2015). The Primer-BLAST program (Ye et al, 2012) was used to check primer-pair specificity of Pr77/Pr78 against two National Center for Biotechnology Information (NCBI) databases: nucleotide collection and genomes from all available organisms.…”

“…The reference PinsEXO1 gene sequence (GenBank accession number GU994093) was used to retrieve orthologous sequences from the genomes of P. aphanidermatum, P. arrhenomanes, P. irregular, P. iwayamai, P. ultimum and P. vexans, deposited in the FungiDB database (Stajich et al, 2012). All PinsEXO1 (n518; Table 1) and orthologous (n57) sequences from other Pythium species were aligned by CLUSTAL W (Larkin et al, 2007) and visualized by MView (Brown et al, 1998).…”