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The macroevolutionary impact of epigenetics and lateral gene transfer on eukaryotic genomes

Periodic Reporting for period 2 - Macro-EpiK (The macroevolutionary impact of epigenetics and lateral gene transfer on eukaryotic genomes)

Reporting period: 2020-09-01 to 2022-02-28

Life on Earth is comprised into three major domains of life: Bacteria, Archaea and Eukaryotes. The former two encompass microorganisms of simple cellular organisation, whereas Eukaryotes display a large number of complex subcellular compartments and molecular machineries. The evolutionary origin of this cellular complexity remains one of the most challenging questions in biology. Due their size and obviousness in nature, large multicellular organisms (such as animals, plants and fungi) are the best-studied eukaryotes, but the overwhelming majority of eukaryotic diversity corresponds in fact to eukaryotic microbes (“protists”), and all multicellular species descend from protist ancestors. Protists are thus of profound ecological and evolutionary importance: the evolutionary history of protists is closely connected to the evolution of the eukaryotic cell itself. Protists inhabit very diverse environments (including most bodies of water, where they can represent important players in the ecosytems). They display an astounding diversity of lifestyles (photosynthetic, parasitic, free-living, feeding on bacteria or on other microbial eukaryotes), adaptations to environments (some are able to live without oxygen, in high salt conditions, at very low or high temperature...) and complex life cycles.

Nonetheless, most protistan groups are very poorly understood, especially if they are non-parasitic. Few protists have been sequenced to obtain their genome, limiting our understanding of their true diversity and our investigation of eukaryotic origin and evolution at large.

The overarching goal of my project is to characterize the genomes of understudied eukaryotic microbes selected for their diversity, and to analyse them using state-of-the-art bioinformatic methods. In particular, we are interested in “uncultivated protists”, meaning organisms that are not easily cultivable in the lab and are thus understudied. For this, we are using “single-cell techniques” and novel genome-scaffolding approaches which allow us to sort cells of interest directly from environmental samples, or from complex cultures (i.e. cultures containing the organism of interest but also many other species).

Having access to the genomic sequence of novel, diverse, understudied protists allows us to tackle many questions in evolutionary biology. Among these, we are praticularly interested in understanding the diversity and evolution of the epigenetic toolkit. Eukaryote genome architecture varies in size and structure. This diversity is only possible due to a well-developed epigenetic toolkit, which allows a tight control of DNA expression. However, almost nothing is known on this topic outside of animals, plants and fungi. The scarce data coming from protists concern parasitic lineages; they indicate large differences with what is known in model organisms. Overall, the characteristics of epigenetic modifications remain a 'black box' in the vast majority of eukaryotic lineages, hampering our
understanding of their evolution and the real extent of their role in shaping eukaryotic genomes. Here we aim to clarifying the evolution of epigenetic mechanisms in eukaryotes through comparative
genomics and experimental approaches, to understand the role of this regulatory process during
eukaryotic genome evolution.
Since the beginning of the project, we have been able to sample, identify, and isolate a dozen novel species representative of an extremely diverse and understudied group of protists. So far, no genomic data is available for this group. Here we used a combination of single-cell sorting (since we cannot grow these organisms in pure culture as feed on bacteria), and sophisticated sequencing approaches to generate genomic data for 7 species. We are now in the process of analyzing these genomes.

One aspect of this project consists in improving our understanding of the deep evolutionary relationships between major clades of eukaryotes. A community effort has yielded the development of a user-friendly tool to better resolve the eukaryotic Tree of Life. This has been published in PLoS Biology (Tice et al. 2021).

Another aspect of our work has been to investigation of the evolution of specific proteins that are involved in epigenetic systems.

Finally, we have developed a sophisticated pipeline that aims to identify the presence of foreign DNA into eukaryotic genomes and investigate prominent characteristics of transferred genes and how they might have impacted the evolution of the recipient species.
Several advances beyond the state of the start have come out so far:
1) The cultivation of protists from a very diverse group almost entirely unknown so far.
2) The development of successful protocols of cell sorting and genome sequencing of protsits from complex cultures.
3) The development of an effective protocol for investigating epigenetic modifications for non-model organisms.
Complex eukaryotic cell and its endomembrane organization