The genome portal of the Department of Energy Joint Genome Institute

Abstract

The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource.

Figure 1.

The Genome Portal page. A pull-down menu for the ‘Fungi’ branch of Eukaryota is shown. Search, BLAST and Download functions are available for the entire selected group. Each genome is linked to the organism page in the related resources, such as Mycocosm and IMG. ‘Project list’ on the top leads users to the list of all sequencing projects at the DOE JGI. The bottom portion of the page connects to the specialized databases for microbes (IMG) and metagenomes (IMG/M), fungi (MycoCosm) and plants (Phytozome).

Figure 2.

The MycoCosm home page includes genome search function and displays major branches of the Fungal Tree of Life with nodes representing phylogenetically related groups. Clicking on a node brings up drop-down menu (shown on lower right) linked to an integrated comparative view (e.g. Mucoromycotina), individual comparative tools (search, BLAST, download) and the list of sequenced genomes from this group, each linked to its own genome-centric view.

Figure 3.

Genome-centric view of the MycoCosm includes several tools (listed in the top menu) and illustrated here by Genome Browser (on top), Synteny by interactive VISTADot plot (lower left) and KOG functional profile (lower right). Genome Browser tracks shown for a thermophile Thielavia terrestris (14) include GC content (light blue), VISTA-based genome conservation (blue and red curve), automatically predicted (blue) and manually curated (red) gene models, transcriptomics (light green) and proteomics (dark green) data, PFAM domains (orange), BLASTx hits against proteins of related organism (blue), and repeats (black). Dot plot is based on VISTA whole genome alignments of two genomes and interactively displays syntenic blocks (collinear in blue or anti-sense in red). KOG profile summarizes functional annotations of genes according to this classification and allows comparison of gene counts in each category between related genomes (last two columns).

Figure 4.

MycoCosm comparative view includes several functions designed for analyzing groups of genomes (listed in the top menu) as illustrated by Cluster view. The Cluster front page (on top) lists two largest clusters of genes conserved in all four Eurotiomycetes and expanded in Aspergillus aculeatus, after using filters (1+:1:1:1). Cluster details page (on bottom) shows six members of the cluster 892, their intron–exon gene structures (right column), PFAM domain composition (pie chart in the middle, no predicted domains here) and species-reconciliated gene tree suggesting two gene duplications Aspergillus carbonarius (red nodes D on the tree in the middle).