ZH Seminars Bioinformatics - Marija Dmitrijeva

Setting up a pipeline for horizontal gene transfer detection

Abstract In addition to vertically transferring genes to their descendants, bacteria can horizontally transfer genes to other members in their community. These horizontally transferred genes frequently confer various selective advantages to the recipient such as antibiotic resistance and the ability to scavenge rare nutrients. Thus, gaining insight into the principles behind horizontal gene transfer is important for understanding the evolution of prokaryotic genomes.

Multiple factors have been shown to affect the rate of horizontal gene transfer. First, the genetic relatedness of the donor and recipient plays a role. Second, bacteria in host-associated environments such as the human gut tend to participate in horizontal gene transfer more often. Finally, bacteria associated with the same environment tend to participate in horizontal gene transfer more often than bacteria from different environments.

In this project, we would like to carry out a global detection of horizontal gene transfer events and investigate the link between horizontal gene transfer rate, species co-occurrence, and species interactions using the ecological data from the Microbe Atlas Project. During my presentation, I will introduce the project and our current ideas, as well as the difficulties I have encountered while setting up the pipeline for horizontal gene transfer event detection.

Links

@mbaudis 2020-04-16
Edit on Github...