Research Group Overview

Thanks to new and cheaper DNA sequencing technologies, bacterial microbial genomes continue to become available
at a rapid pace, enormously increasing the amount of sequencing data available and creating added pressure and
incentive for bioinformaticians to develop new and more efficient sequence analysis computer programs. In
addition to work related to specific genomes (which currently cover the genera Agrobacterium, Azotobacter,
Brucella, Pseudomonas, and Xanthomonas), the Setubal research group is interested in automated genome
annotation, algorithms to help infer bacterial genome evolution, web-based infrastructure for genome annotation
and analysis, and metagenomics.

Pseudomonas syringae is a plant pathogen that has numerous strains that can infect a variety of plants. Some of
these strains cause disease in important agricultural crops, such as tomato. The Setubal group is collaborating
with Boris Vinatzer, assistant professor in the Department of Plant Pathology, Physiology, & Weed Science at
Virginia Tech, on the genomic analyses of Pseudomonas syringae strains. Recently, the two groups identified
several genes in strain T1 that likely play a crucial role in its pathogenicity in tomato plants.

The Setubal group also developed the Genome Reverse Compiler, a bioinformatic tool that played an important
role in the Pseudomonas syringae work. This tool is a computer program that efficiently and automatically
annotates the genes of bacterial genomes. Gene annotation, the process whereby evidence is inferred about the
function of genes, is a key step in genome understanding. Thanks to the Genome Reverse Compiler, the T1 genome
was rapidly annotated, thus providing a foundation for additional work on this pathogen.

Brucella is another class of organisms studied by the Setubal group in collaboration with Stephen Boyle,
professor of microbiology and director of Virginia Tech’s Center for Molecular Medicine and Infectious
Diseases. Brucella bacteria are pathogens that cause serious diseases in humans and animals. By doing a careful
comparative genomic analysis of 10 different Brucella genomes, groups of genes have been discovered that were
likely acquired by an ancestral Brucella and enabled its descendants to become intracellular pathogens. This
discovery was made possible thanks to a novel bioinformatic method developed by the Setubal group to compare
genomic regions from different species.

In addition to work related to specific genomes, the group is also part of a project with Hamza-El-Dorry, from
the American University in Cairo. El-Dorry is leading the Metagenomics Red Sea project, which has collected
biological samples from several locations and depths in the Red Sea. The expectation is that interesting
discoveries about oceanic microbial biodiversity will be made.

Leader: Joao Setubal