Browsing by Author "Dunemann, Sonja Maria"

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    The impact of transposable elements on genomes of parasitic nematodes
    (2020-07-06) Dunemann, Sonja Maria; Wasmuth, James D.; Lynch, Tarah; Deardon, Rob; Yeaman, Sam
    Parasitic nematodes infect many animal and plant species. In humans, they cause significant levels of morbidity and death in low and middle income countries. In livestock and crop plants, they have a significant, negative economic impact, globally. To better understand the biology of these organisms, we must understand their genetic makeup. Up to 36% of parasitic nematode genomes consist of transposable elements (TEs). TEs are mobile, repetitive elements, and act as major players of evolution due to their ability to transfer horizontally between different taxa, move within genomes, and impact the phenotype of their host. However, TEs are often sidelined in standard genomic and transcriptomic analyses. Hence, we know little about their impact on and interaction with nematodes. Here I show that TEs can be horizontally transferred between parasitic nematodes and their hosts, and that TEs are actively mobilizing themselves throughout the life-cycle of two parasitic species. I compare different phylogenetic methods to test for horizontal transfer of TEs between taxa using AviRTE, a LINE element that has been shown previously to have horizontally transferred between birds and parasitic nematodes. I find that phylogenetic trees of TEs based on coding regions differ from trees based on full-length sequences. I identify another TE, RTE1\_Sar, that was horizontally transferred between parasitic nematodes and the common shrew. To rule out contamination of the shrew genome, I develop a pipeline called ConTest that tests for contamination by comparison of TE flanking sequences to two sequence databases. To better understand potential consequences of TE insertions, I investigate underlying mechanism of TE expression. I find that TE expression is specific to developmental stage, and that genes and TEs have potential transcript chimera. This thesis shows that transposons might have transferred more often between parasites and hosts than previously thought, and provides a pipeline to test if a genomic sequence is based on contamination. Furthermore, this work lays an early foundation to study TE impact on parasite genomes by showing that the majority of TE expression arises from read-through transcription, but that younger LINE elements are active and continue to shape genome evolution.