Non-coding RNAs and Conserved Non-coding Elements in Insect Genomes

Abstract

Insects are the largest group within arthropods and in this group various phenotypes and lifestyles can be found. To understand where how this diversity evolved insects are studied on both a morphological and genomic level. The focus of the genomic research lies on protein-coding genes. Genomes, however, consist of different parts with different functions. Only a small fraction (~2 % in humans) is made up of protein-coding genes, whereas the majority of the genome consists of functional parts such as non-coding RNAs (ncRNAs), or regulatory elements, and parts where first evidence shows function but is not yet known what it is, such as conserved non-coding elements (CNEs), transposable elements or repeats. ncRNAs are involved in a plethora of processes in an organism, such as gene regulation, RNA modification and processing, mRNA translation, RNA silencing, and defence against predatory genomic elements. CNEs have been shown to be involved in gene regulation, although the mechanism remains unclear. As stated lies the research focus on protein-coding genes, making most other genomic parts understudied, especially in non-model organisms. In chapter 1 I provide detailed information about the function of different ncRNA classes as well as their functions, and known presence in insects. Regarding the CNEs I also present their background as well as the current state of research. Within this thesis I analyse different Hymenoptera genomes regarding their ncRNA and CNE repertoire. In chapters 2, 3, and 4 I focus on the two species <em>Athalia rosae</em> and <em>Orussus abietinus</em> and categorise their ncRNA repertoire through both homology and <em>de novo</em> analysis. Using the ncRNAs known from other Hymenoptera and present in the databases Rfam and miRBase, I was able to identify a set of ncRNA families that is present in all analysed Hymenoptera. Further <em>de novo</em> analysis of these two genomes showed, that the ncRNA repertoire of miRNAs, tRNAs, lncRNAs, and snoRNAs is larger than shown through the homology prediction alone. This emphasises the importance of not only relying on data present in databases to predict the full ncRNA repertoire of a species, especially in not well studied lineages. Chapters 5, 6, and 7 focus on the identification of CNEs in four Hymenoptera species (<em>Apis mellifera</em>, <em>Athalia rosae</em>, <em>Nasonia vitripennis</em>, and <em>Orussus abietinus</em>). Comparing the genomes using pairwise whole genome alignments I was able to identify numerous CNEs in these Hymenoptera. The CNEs were often found in cluster of at least two (between 76 % and 89 %). My search for genes that are likely associated with these CNE clusters identified a number of lncRNAs as potential interaction partners. Looking at the CNE clusters consisting of more than 10 CNEs and having an lncRNA as the interaction partner, I found these clusters conserved between at least two species. My analysis shows, that these conserved regions can still be identified in lineages with a long divergence time (over 240 million years) as well as a high sequence divergence. Furthermore, the focus of gene interaction partners should be broadened to include non-protein-coding genes. The final chapter provides an overview of the results of this thesis as well as a discussion how my findings fit into the general context of theses fields of research.