MycoCosm portal: gearing up for 1000 fungal genomes

Abstract

MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other 'omics' data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.

Figure 1.

Growth of annotated genomes in MycoCosm. The genomes sequenced by JGI are shown in blue and those sequenced by others are shown in red.

Figure 2.

MycoCosm front page. The MycoCosm tree illustrates relationships between major groups of fungi. Each node of the tree is linked to the corresponding group page and portals for individual genomes within the group.

Figure 3.

Genome Browser for Neurospora crassa. Horizontal tracks represent genomic features of a given assembly scaffold. Red bars indicate N. crassa genes predicted by the Broad Institute and uploaded into MycoCosm. The four tracks with brown bars illustrate SNPs derived from resequencing of mutant strains of N. crassa (7). The two pink curves represent transcriptome profiling using RNA-Seq during N. crassa growth under two different conditions. Additional tracks can be displayed and configured using the toolbar.

Figure 4.

Examples of MycoCosm group pages. A PhyloGroup containing seven annotated genomes of fungi from Mucoromycotina is shown on the left. An EcoGroup with seven annotated genomes of phylogenetically diverse endophytes is shown on the right.

Figure 5.

1000 Fungal Genomes nomination page. Over 500 families of fungi and associated genome projects are displayed. Green and yellow rows highlight families with no, or only one, sequenced genome, where additional species can be nominated for sequencing via the use of the ‘Nominate’ button. Nomination requires user registration and commitment to provide JGI with DNA and RNA samples for sequencing.