Periodic Reporting for period 4 - Macro-EpiK (The macroevolutionary impact of epigenetics and lateral gene transfer on eukaryotic genomes)
Okres sprawozdawczy: 2023-09-01 do 2025-02-28
Life on Earth is divided into three major groups—Bacteria, Archaea, and Eukaryotes. Bacteria and Archaea are made up of relatively simple microbial cells, while eukaryotic cells contain many internal structures and molecular machines that allow for far greater complexity. Explaining how this complexity first evolved remains one of the biggest unanswered questions in biology.
Because they are large and easy to observe, multicellular organisms such as animals, plants, and fungi are the most familiar eukaryotes and the best studied. Yet these groups represent only a tiny fraction of eukaryotic diversity. The vast majority of eukaryotes are microscopic “protists,” and every multicellular species ultimately traces its ancestry back to protist lineages. Protists are therefore central to understanding both the history of life on Earth and the origins of complex cells.
Protists inhabit nearly every environment—from oceans and lakes to soils, hot springs, and oxygen-poor habitats—and they display astonishing diversity. Some photosynthesise, some feed on bacteria or other protists, some are parasitic, and many survive in extreme conditions such as high salinity or low oxygen. Their life cycles and cell structures can be remarkably elaborate. Despite this richness, most protist groups remain poorly understood, especially those that are not parasites. Only a small number have been sequenced, leaving large gaps in our knowledge of their biology and their role in eukaryotic evolution.
The goal of my project is to fill this knowledge gap by characterising the genomes of understudied microbial eukaryotes and analysing them with cutting-edge bioinformatic tools. We focus particularly on “uncultivated protists”—species that cannot easily be grown in the laboratory and are therefore largely unknown. To study them, we use single-cell methods and new genome-scaffolding techniques that allow us to isolate individual cells directly from environmental samples or from mixed cultures containing many species.
Access to the genomes of novel, diverse protists opens the door to answering many questions in evolutionary biology. A major focus of our research is the evolution of the “epigenetic toolkit”—the molecular systems that regulate how DNA is packaged and how genes are turned on or off. Eukaryotic genomes vary enormously in size and structure, and this flexibility is made possible by sophisticated epigenetic mechanisms. Yet almost everything we know about epigenetics comes from animals, plants, and fungi. The limited information available from protists—mostly parasites—already shows that they differ greatly from the standard textbook models.
For most eukaryotic lineages, the nature and function of epigenetic modifications remain almost entirely unknown, leaving a major gap in our understanding of genome evolution. By combining comparative genomics with experimental work, our project aims to uncover how epigenetic systems evolved across eukaryotes and how these regulatory mechanisms shaped the extraordinary diversity of eukaryotic genomes.
Because they are large and easy to observe, multicellular organisms such as animals, plants, and fungi are the most familiar eukaryotes and the best studied. Yet these groups represent only a tiny fraction of eukaryotic diversity. The vast majority of eukaryotes are microscopic “protists,” and every multicellular species ultimately traces its ancestry back to protist lineages. Protists are therefore central to understanding both the history of life on Earth and the origins of complex cells.
Protists inhabit nearly every environment—from oceans and lakes to soils, hot springs, and oxygen-poor habitats—and they display astonishing diversity. Some photosynthesise, some feed on bacteria or other protists, some are parasitic, and many survive in extreme conditions such as high salinity or low oxygen. Their life cycles and cell structures can be remarkably elaborate. Despite this richness, most protist groups remain poorly understood, especially those that are not parasites. Only a small number have been sequenced, leaving large gaps in our knowledge of their biology and their role in eukaryotic evolution.
The goal of my project is to fill this knowledge gap by characterising the genomes of understudied microbial eukaryotes and analysing them with cutting-edge bioinformatic tools. We focus particularly on “uncultivated protists”—species that cannot easily be grown in the laboratory and are therefore largely unknown. To study them, we use single-cell methods and new genome-scaffolding techniques that allow us to isolate individual cells directly from environmental samples or from mixed cultures containing many species.
Access to the genomes of novel, diverse protists opens the door to answering many questions in evolutionary biology. A major focus of our research is the evolution of the “epigenetic toolkit”—the molecular systems that regulate how DNA is packaged and how genes are turned on or off. Eukaryotic genomes vary enormously in size and structure, and this flexibility is made possible by sophisticated epigenetic mechanisms. Yet almost everything we know about epigenetics comes from animals, plants, and fungi. The limited information available from protists—mostly parasites—already shows that they differ greatly from the standard textbook models.
For most eukaryotic lineages, the nature and function of epigenetic modifications remain almost entirely unknown, leaving a major gap in our understanding of genome evolution. By combining comparative genomics with experimental work, our project aims to uncover how epigenetic systems evolved across eukaryotes and how these regulatory mechanisms shaped the extraordinary diversity of eukaryotic genomes.
Understanding how complex eukaryotic cells—like those that make up animals, plants, and fungi—first evolved from simpler microbes is one of the biggest open questions in biology. Although we tend to think of eukaryotes as large organisms, most of their diversity actually comes from microscopic protists that live in oceans, soils, lakes, and many other environments. Many of these organisms are still poorly understood because they are hard to grow in the lab and have no genomic data available, yet they hold crucial clues about our own deep evolutionary history.
The MacroEpik project set out to explore this hidden microbial world by generating new genomic data from rare or deeply diverging protist lineages. Using techniques such as single-cell sequencing, long- and short-read DNA sequencing, metagenomics, and state-of-the-art evolutionary analyses, the project built a large collection of new genomic resources and used them to tackle major questions about how eukaryotes originated and diversified.
A key accomplishment was greatly expanding genomic sampling for several ancient protist groups—such as mantamonads, CRuMs, ancyromonads, Rhizaria, and Preaxostyla. These new datasets made it possible to produce more reliable evolutionary trees and to better resolve some of the earliest branches in the eukaryotic lineage. They also revealed surprising biological and genetic complexity in organisms that were previously known from only a few fragments of DNA.
MacroEpik also helped clarify how eukaryotes are related to their closest known relatives: the Asgard archaea. By adding new genomes and using improved evolutionary models, the project refined the placement of eukaryotes within this archaeal group and provided a clearer picture of the traits and environments that may have characterised the microbes from which eukaryotes arose. Additional studies showed that extremely salt-loving archaea developed their adaptations independently several times, offering insight into microbial evolution in extreme environments.
Another major focus was understanding how key cellular structures evolved. One striking discovery was a mitochondrial genome that is among the most gene-rich ever found outside a small group of protists, and that still contains an ancient protein-transport system thought to date back to the earliest eukaryotes. The project also traced multiple independent paths of mitochondrial reduction—and even complete loss—in anaerobic microbes, and documented surprising conservation of complex cytoskeletal structures across certain parasitic lineages. In red algae, MacroEpik showed that mitochondrial and plastid genomes have repeatedly expanded through the accumulation of introns.
The project also explored how epigenetic mechanisms—systems that regulate gene activity without changing the DNA sequence—vary across eukaryotes. By generating high-quality genomic and transcriptomic data from many protist groups, MacroEpik showed that epigenetic systems are far more diverse than previously thought. Many protists use unique combinations of chromatin proteins, DNA-methylation pathways, and regulatory machinery, suggesting that epigenetics played an important role in early eukaryotic evolution and adaptation.
All datasets produced by MacroEpik were deposited in public repositories and are already being used by other researchers. The team shared results through publications, invited talks, international workshops, and training opportunities for students and early-career scientists.
Overall, MacroEpik has significantly expanded our understanding of microbial eukaryotes and their evolutionary history. By revealing new lineages and uncovering how fundamental cellular systems evolved, the project provides essential tools and insights for future research on the origins of eukaryotes, the evolution of genomes, and the remarkable diversity of life on Earth.
The MacroEpik project set out to explore this hidden microbial world by generating new genomic data from rare or deeply diverging protist lineages. Using techniques such as single-cell sequencing, long- and short-read DNA sequencing, metagenomics, and state-of-the-art evolutionary analyses, the project built a large collection of new genomic resources and used them to tackle major questions about how eukaryotes originated and diversified.
A key accomplishment was greatly expanding genomic sampling for several ancient protist groups—such as mantamonads, CRuMs, ancyromonads, Rhizaria, and Preaxostyla. These new datasets made it possible to produce more reliable evolutionary trees and to better resolve some of the earliest branches in the eukaryotic lineage. They also revealed surprising biological and genetic complexity in organisms that were previously known from only a few fragments of DNA.
MacroEpik also helped clarify how eukaryotes are related to their closest known relatives: the Asgard archaea. By adding new genomes and using improved evolutionary models, the project refined the placement of eukaryotes within this archaeal group and provided a clearer picture of the traits and environments that may have characterised the microbes from which eukaryotes arose. Additional studies showed that extremely salt-loving archaea developed their adaptations independently several times, offering insight into microbial evolution in extreme environments.
Another major focus was understanding how key cellular structures evolved. One striking discovery was a mitochondrial genome that is among the most gene-rich ever found outside a small group of protists, and that still contains an ancient protein-transport system thought to date back to the earliest eukaryotes. The project also traced multiple independent paths of mitochondrial reduction—and even complete loss—in anaerobic microbes, and documented surprising conservation of complex cytoskeletal structures across certain parasitic lineages. In red algae, MacroEpik showed that mitochondrial and plastid genomes have repeatedly expanded through the accumulation of introns.
The project also explored how epigenetic mechanisms—systems that regulate gene activity without changing the DNA sequence—vary across eukaryotes. By generating high-quality genomic and transcriptomic data from many protist groups, MacroEpik showed that epigenetic systems are far more diverse than previously thought. Many protists use unique combinations of chromatin proteins, DNA-methylation pathways, and regulatory machinery, suggesting that epigenetics played an important role in early eukaryotic evolution and adaptation.
All datasets produced by MacroEpik were deposited in public repositories and are already being used by other researchers. The team shared results through publications, invited talks, international workshops, and training opportunities for students and early-career scientists.
Overall, MacroEpik has significantly expanded our understanding of microbial eukaryotes and their evolutionary history. By revealing new lineages and uncovering how fundamental cellular systems evolved, the project provides essential tools and insights for future research on the origins of eukaryotes, the evolution of genomes, and the remarkable diversity of life on Earth.
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.
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.