Many organisms can acquire genetic information outside the normal process of parent-offspring inheritance. This is called horizontal transfer, and while it has been observed all around the tree of life, it is most common in microbes such as bacteria and archaea. In such groups horizontal transfer events often involve clusters of genes with a common function, referred to as genomic islands.
We have developed a software package called xenoGI that takes as input a set of sequenced microbial genomes and a tree specifying their phylogenetic relationships. It then identifies islands that entered via horizontal transfer events, and maps those events onto the phylogenetic tree for the group. Over the last year and a half, we (collaborating with Ran Libeskind-Hadas and students) have included a gene reconciliation model into this software, which allows us to reconstruct not only the insertion of genes via horizontal transfer, but also their subsequent evolution inside the group of microbes.
This summer we want apply this approach to better understand genome evolution in Staphylococcus aureus. S. aureus is an opportunistic pathogen that can sometimes cause quite severe infections. In recent years, many strains of S. aureus have acquired antibiotic resistance (via horizontal transfer). We are interested in taking the many hundreds of sequenced genomes for S. aureus and applying our method to them, to better understand the evolution of pathogenicity and resistance in S. aureus.
The project will involve substantial amounts of programming and data analysis. The student will have the opportunity to creatively develop ways to display data. They will work closely with me, and also with Joe Wirth, the PIC postdoc who is working in my lab now.
In addition to filling out the application on this site, to complete your application for summer research in Biology, please contact me to discuss the project and submit the google form below by Feb 28:
If you enjoy computational work, and want to apply it to evolution and human health, this could be a fun project for you.