Genomic studies of the ribosomal RNA gene locus and the evolution and retrotransposition mechanisms of its mobile elements

The rDNA locus and the non-LTR retrotransposons R1 and R2 that insert specifically into the 28S genes provide a microcosm to study the interactions between mobile elements and the host genome. While the rRNA genes are not assembled as part of completely sequenced genomes, the explosion in whole genome sequencing projects provided the raw sequencing reads used throughout the research presented in this thesis. These sequence data are used to address three issues: the pattern of nucleotide variation present in rDNA loci, the evolution of R1 and R2, and the mobility mechanisms of these elements.;Concerted evolution of the rDNA locus was studied in 11 Drosophila, one Nasonia and nine non-arthropod species. The Drosophila, Nasonia and five of the non-arthropod species contained low levels of sequence variation (less than 0.2%). Four non-arthropod species contained higher levels of variation that suggested the presence of multiple rDNA loci that undergoes separate concerted evolution. The most complete analysis was done in Drosophila where nucleotide variants were generally found to be more numerous in faster evolving regions of the rDNA unit. The one deviation from this pattern was the higher nucleotide variation found in the 18S genes than in the faster evolving 28S genes.;The R1 and R2 elements in twelve Drosophila species displayed a spectrum of sequence variation within species suggesting the formation of nascent R1 and R2 lineages, a prerequisite for the evolution of multiple families often seen within species. The Nasonia species contained 11 R1 and R2 families in the three closely related species. The different R1 and R2 families of Nasonia appear to use parts of the retrotransposition machinery of other families, perhaps providing a mechanism to help maintain the many competing element families. While R1 presence is limited to arthropods, a survey of eukaryotes showed R2 elements present in most animal groups except mammals. The common ancestor of bilateria and cnidaria appeared to have two R2 families, suggesting R2 genesis may have occurred over 1 billion years ago. The search for R1 and R2 elements revealed the first examples of non-autonomous SINE-like elements that appeared to use the R1 and R2 machinery for retrotransposition. Non-arthropod R2 elements displayed characteristics not previously observed among the more studied R2 elements in arthropods, most significantly the evolution of new target site preferences.;Finally, junction analysis of R1 and R2 elements from 12 Drosophila, three Nasonia and 11 non-arthropod species suggested that during the integration reaction of the elements the DNA strand generated by reverse transcription is positioned to anneal to the upstream target site prior to initiating second strand synthesis. 5' junctions are precise when the reverse transcribed strand can anneal to the upstream target, otherwise the junctions are variable. Most interesting were the R2 families within non-arthropods with 5' junctions 1000's of bp upstream within the rDNA unit of the 3' junctions. These unusual families encoded three N-terminal zinc fingers, while R2 families with one zinc finger showed no target site evolution. This suggests dramatically different binding sites for the R2 subunit that cleaves the top strand.