Genome dynamics in early eukaryotic evolution: importance of enigmatic lineages

The origin of the eukaryotic cell from its bacterial ancestor is probably the most complex transition in evolution. Understanding the mechanisms of, and reasons for this major evolutionary transition is of fundamental importance for cellular and evolutionary biology. To reconstruct the origin and evolution of the eukaryote cell one needs to study the changes that have occurred to an organisms hereditary information (genome) over time; from primitive to modern organisms. Recent improvements to the eukaryote tree of life have divided organisms it into a small number of supergroups. These supergroups encompass the majority of living eukaryotes but there are still some enigmatic species that place external to these known groupings. Some of these species represent our earliest ancestors, and as such, are of major importance to understanding how the eukaryotic cell has evolved. Projects that map eukaryotic genomes are yet to study a species outside the known supergroups. Though, such a genome will give insight and resolution into how eukaryotes have evolved from a bacterial ancestor toward advanced organisms. The overall objective of this project is therefore to explore the dynamics of genome changes that have occurred during evolution. Cultures of multiple enigmatic species/strains have been grown (initially in Japan then Norway) and high quality gDNA and RNA successfully isolated from cultures or single-cells. Genomic data from multiple enigmatic eukaryotes and their prokaryotic prey (metagenomes) have been sequenced (Illumina and PacBio). The metagenomes have been assembled to their separate genomes and functionally annotated in collaboration with VIB in Belgium. Multiple bacterial genomes are now published, with more in-prep. The eukaryotic genomes, both nuclear and mitochondrial are also in-prep and will be published in the near future. These will represent the deepest eukaryotic genomes available. Additionally, I have published results showing the diversity and distribution of one of these deep enigmatic groups "Diphyllatea" using PacBio to sequence samples from different environments.

The origin of the eukaryotic cell from the prokaryotic ancestor is probably the most complex transition in evolution. Understanding the mechanisms of, and reasons for this major evolutionary transition is of fundamental importance for both cellular and ev olutionary biology. To reconstruct the origin and evolution of the eukaryote cell one needs to focus on the genomic changes that occurred in deep eukaryotic lineages. Recent improvements in the eukaryote tree of life have divided it into a small number of so-called supergroups, comprising Opisthokonta, Amoebozoa, Archaeplastida, Excavata, SAR and Hacrobia. These supergroups encompasses the majority of extant eukaryotes, but there are still some enigmatic/orphan lineages that have unclear affinity. The dee p evolutionary placement of these lineages is of major importance to understanding eukaryotic evolution. Eukaryotic genome projects are yet to sequence a lineage of unknown affinity. The genomic sequencing, and subsequent comparison of such deep eukaryoti c genomes will give insight and resolution into how eukaryotes have evolved from a prokaryotic ancestor toward Opisthokonta. The overall objective of this project is therefore to explore the dynamics of genomic changes that have occurred in eukaryotic evo lution. This will be investigated by genome sequencing numerous deep eukaryotic lineages with enigmatic positions. These genomes will then be compared to other eukaryotic genomes. The project builds on recent developments in eukaryotic whole genome amplif ication and comparative genomics to focus on fundamental questions about the origin and evolution of eukaryotes. The project can therefore have significant bearing on central evolutionary issues and further our understanding of the genomic dynamics that h ave occurred during eukaryotic evolution. The project will increase general understanding of processes that have formed eukaryote diversity contributing to scientific advancement in several areas of biology.