Transposable elements (TEs), so called “jumping-genes”, are DNA sequences that are able to proliferate in the genomes of organisms. Their movement in the genome can be disruptive by inserting either into or near genes, but sometimes they provide beneficial mutational variation that natural selection, the ultimate force in evolution, can act upon. Despite their potential benefits for the organism, their overall movement is often thought to be at odds with the rest of the genome leading to them having been referred to as selfish. To counteract the negative effects of TE’s movement, hosts have evolved defenses to control and prevent TE-related damage. In this thesis, I have studied TEs in fungi and their interaction with a fungal specific defense called repeat induced point mutation (RIP). RIP induces C-to-T mutations in any repeated region of the genome, including both TEs and duplicate genes. One of the key species where RIP has been described is the filamentous ascomycete Podospora anserina, which has been used as a model organism within genetics and evolution for over a century. In chapter I we were able to dive deeply into the interaction between a specific TE called crapaud and its evolutionary history, and discuss its potential interaction with RIP. In chapter II we discovered that RIP have been lost in a close relative to P. anserina called Podospora pseudocomata and that this loss may have been the cause of a total shift in both types and amount of TEs in its genome. This species also has smaller centromere regions than P. anserina. The centromere regions are the anchoring points when the chromosomes are pulled apart in every cell division. In many fungi the DNA of this region contains many TEs, and our result hints at a connection between the centromeres and RIP. P.anserina and P. pseudocomata are both part of an order known as Sordariales, which have species important to industry and contain model organisms such as P. anserina and Neurospora crassa. In chapter III we compared the genomes of nine families from this order using whole genomes and constructed a phylogeny of the order using phylogenomics. In chapter IV we developed in-depth methods to continue investigating RIP in the order Sordariales and discovered that P. pseudocomata is not the only species that has lost the RIP mutation pattern. We find 17 species lacking RIP, spread across the Sordariales phylogeny. In conclusion, this thesis presents a glimpse into the world of TEs and host genomes and their defense against TEs in filamentous ascomycetes, and the balance and conflict between them.

Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally. 

Background The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance of retrotransposons compared to other interspersed repeats. The LTR-retrotransposon family crapaud is particularly abundant in the genome, and consists of multiple diverged sequence variations specifically localized in the 5' half of both long terminal repeats (LTRs). P. anserina is part of a recently diverged species-complex, which makes the system ideal to classify the crapaud family based on the observed LTR variation and to study the evolutionary dynamics, such as the diversification and bursts of the elements over recent evolutionary time.Results We developed a sequence similarity network approach to classify the crapaud repeats of seven genomes representing the P. anserina species complex into 14 subfamilies. This method does not utilize a consensus sequence, but instead it connects any copies that share enough sequence similarity over a set sequence coverage. Based on phylogenetic analyses, we found that the crapaud repeats likely diversified in the ancestor of the complex and have had activity at different time points for different subfamilies. Furthermore, while we hypothesized that the evolution into multiple subfamilies could have been a direct effect of escaping the genome defense system of repeat induced point mutations, we found this not to be the case.Conclusions Our study contributes to the development of methods to classify transposable elements in fungi, and also highlights the intricate patterns of retrotransposon evolution over short timescales and under high mutational load caused by nucleotide-altering genome defense.