Identification and annotation of recombinant repeats in mammals indicates they are experimental products for creating novel transposable element families.

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.

Author dc:creator

• Lim, Sim Lin

Advisors dc:contributor.advisor

• Adelson, David Louis
• Scott, Hamish Steele

• transposable elements; repeats; evolution

Handle dc:identifier.uri

http://hdl.handle.net/2440/85194

OAI identifier oai:identifier

oai:digital.library.adelaide.edu.au:2440/85194