Exploring genome reduction to reconstruct the minimal gene set necessary for life

Background

Historically, there has been an interest in reconstructing the minimal set of genes necessary for life, especially to build a synthetic cell. The search for such a minimal genome has largely been informed by the Mycoplasma group, a bacterial lineage including parasites of humans and other animals. However, genome reduction – the substantial loss of genes – also occurs in many other prokaryotes. For example, genome reduction is known in endosymbiotic prokaryotes, bacteria abundant in the ocean surface (e.g. Prochlorococcus and Pelagibacter) and certain extremophiles. However, many unexplored lineages may have experienced genome reduction but have been overlooked. Exploring these lineages will improve our understanding of genome reduction, which informs the reconstruction of a minimal gene set for prokaryotic life.

Key questions

• Which prokaryotic lineages underwent genome reduction?
• What forces underly genome reduction in different lineages?
• Does lifestyle impact which genes are lost?
• Which genes are needed for a minimal prokaryotic cell?

Techniques

• Comparative genomics
• Phylogenomics
• Command Line scripting
• Programming (Python, R, bash)

BSc/MSc theses

This project is available for BSc or MSc students interested in phylogenomics and comparative genomics. Experience with working on Linux command line and programming (especially Python, R or bash) is appreciated. If you are excited about genome evolution and interested in this project, feel free to contact me via the contact form