Multicellular organisms (e.g., animals, plants and fungi) are the best-studied eukaryotes but their ancestors and the vast majority of eukaryotic diversity correspond to microbial species (“protists”). 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: 1) reconstructing a robust phylogeny of eukaryotes; 2) tracing the evolution of genes involved in epigenetic mechanisms and obtaining epigenomic maps from under-studied protists; 3) investigating the intriguing hypothesis of a possible interplay between epigenetic regulation and horizontal gene transfer and its influence on eukaryotic genome evolution.
To achieve this, we will characterize the transcriptomes, genomes, methylomes and small RNAs of understudied eukaryotic microbes selected for their key phylogenetic position, and analyse them using state-of-the-art bioinformatic methods. We will target uncultivated protists, using single-cell techniques and novel genome-scaffolding approaches.