| Summary: | This thesis presents comparative genomics studies in insects as well as bioinformatics software development. Its empirical research part is focused mainly on mobile genetic elements, also termed transposable elements. The data basis contains datasets from public repositories, a rich and often underexplored source of information on genomic biodiversity. Transposable elements in particular are often neglected when the results of a genome sequencing study are published, although they make up a major part of virtually every eukaryotic genome. After a general introduction in Chapter 1, I characterize and compare the transposable element repertoire of 73 arthropod species in Chapter 2 and find that it correlates to genome size in both abundance and diversity. In Chapter 3, I study the effect of transposable elements on the evolution of genome size in more detail and on an expanded dataset of 96 species. In Chapter 4, I present a software pipeline for delineating orthology among coding nucleotide sequences, an essential tool for many comparative and phylogenetic studies. Finally, Chapter 5 is a general conclusion. Chapter 2: Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6 % in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58 % in the malaria mosquito (Diptera) and the ...
|
|---|