Lateral gene transfers between closely related eukaryotes
6 month Master’s student project
Background
Horizontal gene transfer, also called lateral gene transfer or LGT, allows the acquisition of 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 contrast, the role and frequency of LGT in eukaryotes has been much less studied, although there are clear examples of its impact on the evolution of certain unicellular eukaryote parasites. When they exist, these recent studies often focus on gene transfer events from very distant organisms, such as from bacteria, because they are easier to detect with confidence. However, it has been shown in bacteria that LGTs more often occur among closer related lineages. This can be explained in part because horizontally acquired genes that use codons that better match the codon usage of their new host genome will be better optimized for expression within the context of that genome and will confer less of a fitness cost on their new host. . In eukaryotes, the extent to which closely related organisms exchange genetic material and how much this varies across the diversity of eukaryotic lineages is, in contrast, limited.
Project
This project aims to estimate the importance of LGT between closely related eukaryotic species. It consists of two parts: A) developing an approach that detects genes that are very likely to be derived laterally from a different, but closely related eukaryote, and B) using this approach to study which eukaryotic clades underwent many of such ‘short-distance’ LGTs andto identify the features (such as function or codon usage) of genes shared via LGT between closely related species. The developed approach will first be benchmarked with a set of published LGTs, and will then be applied to identify cases of LGTs in understudied lineages of unicellular eukaryotes (protists).
Your profile
Ideally, the candidate will have some knowledge in phylogenetics/molecular evolution and some knowledge or strong desire to learn scripting (Python or Perl) and working in a linux environment. Additional requirement: good level in English, good oral and written communication skills, autonomy, organization skills.
Practicalities
This is a 6 month internship that will take place between January and June 2021. A financial compensation of €577.50/mo is offered.
The research unit of “Ecology, Systematics and Evolution” (ESE) is located in the University Paris-Sud campus in Orsay. This campus is 20 km south of Paris and well connected through commuter train.
The student will work within the DEEM (Diversity, Ecology and Evolution of Microbes: http://www.deemteam.fr/en) team, which has a broad expertise in ecology and evolutionary biology, with a focus on microbes (prokaryotic and eukaryotic). This internship will be co-supervised by Dr. Laura Eme (laura.eme@universite-paris-saclay.fr), principal investigator, and Dr. Jolien van Hooff, postdoctoral fellow (jolien.van-hooff@universite-paris-saclay.fr).
Note the possibility to apply for a PhD scholarship from the doctoral school at the end of the internship if you are interested in pursuing a PhD with us.
Interested?
If you are interested in genome evolution and pursuing a research project in bioinformatics and phylogenetics, please contact Dr Laura Eme (laura.eme@universite-paris-saclay.fr) for more information or apply directly by sending your CV and a cover letter explaining your motivation for undertaking this project.