Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/85194
Type: Thesis
Title: Identification and annotation of recombinant repeats in mammals indicates they are experimental products for creating novel transposable element families.
Author: Lim, Sim Lin
Issue Date: 2014
School/Discipline: School of Molecular and Biomedical Science
Abstract: About 40-50% of mammalian genomes are made up of repetitive elements, primarily transposable elements. Transposable elements' activities not only drive genome evolution, they contribute to the creation of novel recombinant repeats. Recombinant repeats have largely remained uncharacterized due to their complexity. Initially, I developed a pipeline for the genome wide identification of recombinant repeats in four different mammals: human, mouse, cow and horse. The pipeline identified 1,336,824 copies, but only 37,830 sequences were able to be clustered into 6,116 families. The majority of the recombinant repeats were simple recombinant repeat families and only a small proportion were complex recombinant repeat families. My analysis showed that recombinant repeat families only covered a small fraction of the genomes examined (0.30% in human, 0.13% in mouse, 0.217% in horse and 0.464% in cow), indicating most of the recombinant repeats were singletons. Further analysis has shown that both classes of RR were created via transposon-into-transposon events, indicating that novel transposable elements are likely to be created via this mechanism. I found that simple recombinant repeats were probably retrotranspositionally active because they contained polyA tails and target site duplications, showing that they integrated into the genome via retrotransposition events. However, complex recombinant repeat families were only replicated via segmental duplications. My analysis showed that complex recombinant repeat families are excellent candidates for the identification of genome segmental duplication regions that cannot be found through standard methods. In addition, I used the RR identification pipeline to annotate possible RR in pig genome. I discovered a novel RR family (LTR2i_SS) that contained > 1,000 copies. Repeat annotation showed that it was a chimeric LTR2_SS that contained ~300bp of un-annotated sequence, only found in the pig genome. Further investigation revealed that some LTR2i_SS flanked β3 proviruses, but these proviruses were unable to replicate autonomously as they did not encode a functional, complete polyprotein. My phylogenetic tree analysis of the LTR2i_SS and LTR2_SS familis suggested that LTR2i_SS was the ancestral form of LTR2_SS. In conclusion, I was able to identify the recombinant repeat distributions in different mammals and determine their most probable origin as TinT events. I have shown that recombinant repeats could serve as an important model to explain the origin of novel transposable elements in genomes, or could be used as markers to identify structural variations, or segmental duplications in different species. However, my data have also shown that we have to be cautious when annotating novel recombinant repeats in genomes, as they could be the ancestral form of other known transposable elements rather than novel forms generated through TinT.
Advisor: Adelson, David Louis
Scott, Hamish Steele
Dissertation Note: Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2014
Keywords: transposable elements; repeats; evolution
Provenance: This electronic version is made publicly available by the University of Adelaide in accordance with its open access policy for student theses. Copyright in this thesis remains with the author. This thesis may incorporate third party material which has been used by the author pursuant to Fair Dealing exceptions. If you are the owner of any included third party copyright material you wish to be removed from this electronic version, please complete the take down form located at: http://www.adelaide.edu.au/legals
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