Project

Tracing the ins & outs of horizontal gene transfer in eukaryotic microbes

Using bioinformatics to investigate how horizontal gene transfer affects the evolution of unicellular eukaryotes, such as its scale, significance and features.

Background

Horizontal gene transfer (HGT) allows an organism to acquire new genetic material, and thus new functions, from distantly related organisms. This process is well known to be a major driver of evolution in prokaryotes, and is for example responsible for the acquisition of antibiotic resistance in bacteria.

 
In eukaryotes however, HGT has been much less studied. Yet there are sound examples of its impact on the evolution of eukaryotes, for example of unicellular eukaryotic parasites. Overlooking different studies, a recent review concluded that no less than 1% of the genes of eukaryotic microbes were gained by HGT events - mostly from bacteria.


We hypothesize that this 1% might even be an underestimation, for example because they are often limited to HGTs donated by bacteria. Due to new data, we are now able to expand our HGT examinations, and thereby obtain a comprehensive overview of HGT in eukaryotic microbes.

Aims

  • Develop approaches to detect different types of HGTs:

    • HGTs between distantly related (e.g. from bacteria to a eukaryotic species) and closely related organisms
    • More recent and more ancient HGTs

  • Characterize HGT in various eukaryotic microbes, for example:

    • How frequent is HGT and how many genes result from HGT?
    • What sort of functions do the transferred genes hold?

  • Shedding light on the impact of HGT on the evolution of eukaryotic microbes, such as:

    • When, on the tree of life, did many HGTs occur?
    • Do such ‘bursts’ coincide with specific evolutionary transitions, for example from a free-living to a parasitic lifestyle? May HGTs have facilitated such transitions?

Techniques

Bioinformatics techniques, such as sequence similarity searches (BLAST, HMMer, Interproscan, etc.) and phylogenetics, as well as programming in Python.

BSc/MSc theses

Thesis projects are available for BSc or MSc students with interest in evolutionary microbiology and bioinformatics. Experience with working on linux command line and programming (e.g. Python, R) is appreciated.

Contact

Are you interested in working on this project? Please contact Jolien van Hooff