Transposable elements (TEs) are DNA sequences that have the ability to replicate within a genome using a variety of mechanisms. They are present in almost all eukaryotic genomes, and they play an important role in genome evolution by creating genetic variation through their mobility. TEs can be divided into two classes (I and II) based on their replication mechanism.
Class I elements use an RNA intermediate for transposition and are called retrotransposons. They can be further subdivided into LTR and non-LTR elements, named after the presence or absence of long terminal repeat (LTR) sequences in the element. Class II elements use a DNA intermediate and are therefore called DNA transposons. The evolutionary factors that influence transposable element abundance have received considerable attention but are still not fully understood. In my thesis I have focused on three different projects concerning the evolutionary dynamics of TEs.
In my first project I analyzed the evolutionary dynamics of the LTR family roo and it's highly diverged relative rooA in 12 closely related Drosophila species. Roo is the most abundant retrotransposon in the fruit fly Drosophila melanogaster. Its evolutionary origins and dynamics are thus of special interest for understanding the evolutionary history of Drosophila genome organization. Within the 12 genomes I found a broad spectrum for the evolutionary dynamics of roo and rooA ranging from recent intense transpositional activity to slow decay and extinction.
Furthermore I suggest an origin of roo/rooA within the Drosophila clade based on the balance of phylogenetic evidence, sequence divergence distribution, and the occurrence of solo-LTR elements.
The second project in my thesis regards the BEL/Pao subclass of LTR retrotransposons. LTR elements are the most abundant class of TEs. In contrast to the other subclasses of LTR elements, little attention has been paid to elements belonging to the metazoan BEL/Pao subclass. I
therefore searched for all BEL/Pao elements in a set of 62 metazoan genomes and analyzed their evolutionary history. My work shows that BEL/Pao elements are the second most abundant class of LTR retrotransposons in metazoan species and are therefore much more frequent than I previously thought. Furthermore, I identified two novel BEL/Pao superfamilies. The presence
of BEL/Pao elements in both metazoan kingdoms suggest that they arose during early metazoan evolution. In my third project I studied the in
uence of the mating system on TE dynamics in the predominantly
selfing plant A. thaliana and its close outcrossing relative A. lyrata. There are two opposing hypotheses that make predictions regarding the impact of selfing and outcrossing on TE abundance. The first predicts a higher TE number in a selfing species due to less ectopic recombination that eliminates TE copies. The second predicts a lower TE number in selfing species, because TEs can spread more easily in outcrossing species through recombination. I conducted the �first genome-scale analysis regarding the influence of the mating system on TE abundance. I identified more than three times more TE copies in the outcrossing A. lyrata than in the selfing A. thaliana, as well as ten times more TE families unique to A. lyrata. On average, elements in A. lyrata are younger than elements in A. thaliana. In particular, A. thaliana shows a marked decrease in element number starting approximately 0.5 million years ago, around the time predominant selfing originated. My observations suggest that if the mating system is an important factor in determining TE copy numbers, then selfing species are likely to have fewer transposable elements.