Dynamics of Transposable Elements

Life is a struggle for survival where, for example, parasites prey on their hosts and hosts combat their parasites. Surprising to many, this battle also rages in our genomes. Parasitic DNA spreads in our genomes, even if this is harming our health. These p arasitic sequences, also called transposable elements (TEs), have been remarkably successful, constituting more than 50% of our human genomes. TEs do not only spread within but may also spread between species. A vivid example is the blood feeding bug Rhodnius prolixus which likely transferred several of its TEs to opossums. Upon entering a novel species TEs often spread in host populations, but an uncontrolled spread of the TE could drive the host population to extinction. Therefore species have developed sophisticated defence mechanisms to stop the spread of TEs. In many species it is assumed that a TE invasion is stopped when the TE randomly jumps into a certain genomic region, the so-called piRNA clusters. These clusters act like traps in the genome. Once the TE jumps into a cluster, small RNAs, the piRNAs, will be produced that silence the TE. Recently some doubts emerged about this model, therefore it is not clear if we truly understand the central open question on how TEs are silenced in species. If t his trap model is true our computer simulations predict that piRNA clusters should contain at least two insertions from each TE family and have a highly variable composition among individuals of a population. Here we will test these predictions in two Drosophila species by sequencing the genomes of several individuals using novel long-read sequencing technology. This novel technology finally enables us to accurately sequence repeat-rich and complex genomic regions, such as piRNA clusters. Furthermore it is an important open question whether the host defence, for example acting through piRNA clusters, is the only mechanism stopping TE invasions. It is for example possible that evolutionary processes, such as negative selection, also decisively contribute to stopping TE invasions. This can be easily understood if we for example assume that each TE insertion makes a fly less sexy, then flies with many TE insertions will find fewer mates and thus have fewer offspring. As a result TE insertions will be negatively selected. Such negative selection leads to certain signatures in genomes that can best be identified using high-quality genomes sequenced with the long-read technology. We will thus use our sequences from the two Drosophila species and ask if we find evidence that negative selection contributes to stopping TE invasions. So far no software exists that enables this analysis. We will therefore also develop a novel tool for comparing and visualizing the TE composition among sequences of many individuals.