The impact of transposable elements on genomes of parasitic nematodes

Dunemann, Sonja Maria

The impact of transposable elements on genomes of parasitic nematodes

dc.contributor.advisor	Wasmuth, James D.
dc.contributor.author	Dunemann, Sonja Maria
dc.contributor.committeemember	Lynch, Tarah
dc.contributor.committeemember	Deardon, Rob
dc.contributor.committeemember	Yeaman, Sam
dc.date	2020-11
dc.date.accessioned	2020-07-09T21:33:50Z
dc.date.available	2020-07-09T21:33:50Z
dc.date.issued	2020-07-06
dc.description.abstract	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.	en_US
dc.identifier.citation	Dunemann, S. M. (2020). The impact of transposable elements on genomes of parasitic nematodes (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.	en_US
dc.identifier.doi	http://dx.doi.org/10.11575/PRISM/37991
dc.identifier.uri	http://hdl.handle.net/1880/112269
dc.language.iso	eng	en_US
dc.publisher.faculty	Veterinary Medicine	en_US
dc.publisher.institution	University of Calgary	en
dc.rights	University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.	en_US
dc.subject	Transposable elements	en_US
dc.subject	Horizontal transfer	en_US
dc.subject	Nematodes	en_US
dc.subject.classification	Bioinformatics	en_US
dc.subject.classification	Genetics	en_US
dc.subject.classification	Parasitology	en_US
dc.title	The impact of transposable elements on genomes of parasitic nematodes	en_US
dc.type	doctoral thesis	en_US
thesis.degree.discipline	Veterinary Medical Sciences	en_US
thesis.degree.grantor	University of Calgary	en_US
thesis.degree.name	Doctor of Philosophy (PhD)	en_US
ucalgary.item.requestcopy	true	en_US