Network visualisation of genomic transposable element content for comparative analysis

Abstract

Transposable elements (TEs) are discrete DNA sequences that multiply and move within their host genomes. These elements are widespread across eukaryotic species and occupy over 50% of the human genome, however their abundance and diversity vary widely between species. The factors shaping the differences in TE content are poorly understood. Investigating the evolution of TEs has its difficulties, because their sequences diversify rapidly and TEs are often transferred through non-conventional means such as horizontal gene transfer. I developed methods for the visualisation and analysis of TE content across a multitude of genomes. Furthermore, I used these techniques to investigate epigenetic mechanisms and their potential role in the evolution of TE abundance and diversity amongst species. First, I constructed a sequence similarity network (SSN) to study the sequence evolution of Tc1/mariner elements across focal nematode species. With this method I was able to identify an unknown connection between two TE families and an associated convergent acquisition of a domain from a protein-coding gene. Second, I developed a weighted bipartite network to investigate how TE content across species is shaped by epigenetic silencing mechanisms. I show that the presence of PIWI-interacting RNAs (piRNAs) is associated with differences in network topology after controlling for phylogenetic effects, indicating higher tolerance of TEs in species with piRNAs. Additionally my analysis of single cell RNA sequencing data from Caenorhabditis elegans embryogenesis gives evidence that some TE families are differentially expressed during C. elegans embryonic development and show cell type specific expression patterns. Together this thesis demonstrates how network-based approaches can be used to identify hitherto unknown properties of TE evolution across species. It gives an insight into the factors responsible for TE diversity, including epigenetic mechanisms and the beneficial effects of TEs for their host genomes.