Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Genetics, Development and Cell Biology


Bioinformatics and Computational Biology

First Advisor

Thomas Peterson


As major components in eukaryotic genomes, Transposable Elements (TEs) have been studied for decades. In the 1950s to 1990s, the predominant opinions considered TEs as “junk DNA” and “selfish elements”. However, subsequent studies showed that TEs are important players in genome dynamics. TEs are presented in many shapes and characteristics in genomes. Generally, two classes of TEs are distinguished by their transposition features: Class I TEs rely on RNA for their transposition, and Class II TEs are independent of RNA intermediates. In this thesis, I focus on the major type of Class II TEs which is called Terminal Inverted Repeat (TIR) elements. While most of the TIR TEs are heavily methylated and are considered inactive, recent studies have shown that in many plant genomes some TIR TE families are still able to transpose. Besides that, in certain situations, different TEs are capable to work together to generate larger rearrangements in genomes. In this thesis, I present our findings of novel TIR activities and the tools we developed to facilitate TE studies. This thesis contains 6 chapters and these results will contribute to our knowledge of TIR TEs in plant genomes.


Copyright Owner

Weijia Su



File Format


File Size

219 pages

Available for download on Saturday, August 28, 2021