The macroevolutionary impact of epigenetics and lateral gene transfer on eukaryotic genomes
Multicellular organisms (e.g., animals, fungi and plants) are the best-studied eukaryotes but their ancestors and the vast majority of eukaryotic diversity correspond to microbial species (“protists”). The evolutionary history of protists is closely connected to the evolution of the eukaryotic cell itself.

However, most protist diversity is still genomically unexplored, limiting our investigation of eukaryotic evolution. For example, while the importance of lateral gene transfer (LGT) in prokaryotic evolution is well recognized, its role in eukaryotic evolution is still debated. In addition, although epigenetic mechanisms represent a hallmark of eukaryotic genome regulation, we know surprisingly little about the evolution of these mechanisms across eukaryotic diversity.

The overarching goal of my project is to understand how epigenetic mechanisms and LGT have shaped the macroevolution of eukaryotic genomes. This project has several inter-related intermediate objectives, which each in themselves will bring crucial insights into eukaryotic evolution: 1) reconstructing a robust phylogeny of eukaryotes; 2) inferring the gene content of the Last Eukaryotic Common Ancestor; 3) tracing the evolution of genes involved in epigenetic mechanisms and obtaining epigenomic maps from under-studied protists; 4) investigating the intriguing hypothesis of a possible interplay between epigenetic regulation and horizontal gene transfer and its influence on eukaryotic genome evolution: Have genes involved in epigenomic mechanisms been transferred between eukaryotes? Do epigenomic modifications affect the frequency of LGT in different lineages?

To achieve this, I will characterize the transcriptomes, genomes, methylomes and small RNAs of understudied eukaryotic microbes selected for their key phylogenetic position, and to analyse them using state-of-the-art bioinformatic methods. I will target uncultivated protists, using single-cell techniques and novel genome-scaffolding approaches.