MicrobesOnline: an integrated portal for comparative and functional genomics

Abstract

Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

Figure 1.

TreeBrowser in gene centric view and species view. (A) The TreeBrowser gene centric view for the E. coli K12 gene purR. The purR gene is shown centered in the browser with the neighboring up- and downstream genes. The phylogenetic tree for the purR gene is shown on the left, with a single representative selected for each clade. (B) The species view for the purR gene. The gene tree is shown on the left and the species tree on the right. Gene tree leaves are labeled numerically and these labels correspond to the comma separated list next to the names on the species tree, indicating which genes are possessed by the species, or species group, in the species tree. In this tree, we can see that the species tree indicates that the purR and rbsR are paralogs of an ancestral duplication event. Additionally, we can see that horizontal gene transfer is a likely explanation for the presence of the rpsR gene in the clade labeled Shewanella—because the gene is present in only one genome out of the 15 species represented by that clade, the could either be one HGT event or multiple independent deletion events.