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.

In the first chapter, I summarize the evolutionary impacts of TIR elements when they mobilize through alternative transpositions. Unlike standard transposition, alternative transposition involves two distinct TEs and generates more complicated genome rearrangements such as deletion, inversion, duplication, and translocation. The first chapter serves as an introduction to alternative transposition. I describe various types of alternative transposition induced by TIR transposable elements and their outcomes.

In the second chapter, I present our results of Composite Insertions (CIs), a novel structure generated by Ac/Ds induced alternative transposition. We used maize pericarp color 1 (p1) and pericarp color 2 (p2) genes as a genetic system to identify CIs. We analyzed their structures and proved our hypothesis that these CIs can regulate gene expression by duplicating and shuffling enhancer elements. Previous studies have shown that transposable elements perform enhancer-like activities. The mechanism behind this function is typically related to the evolutionary forces, which drive TEs evolving into regulatory elements. Also, most of these studies were focused on Class I TEs in animal and human systems. This chapter demonstrates an alternative way of how Class II TEs contribute to gene regulation in maize.

To analyze the larger impact of TIR TEs, we developed a bioinformatics pipeline called TIR-Learner. It is a new ensemble method for TIR Transposable Element annotation. In chapter 3, I introduce the algorithms and methods used in TIR-Learner, and the analysis of Maize TIR elements we performed by using TIR-Learner. TIR-Learner combines the advantages of current homology-based annotation methods with the powerful de-novo machine-learning approaches, resulting in better efficiency and accuracy of TIR element annotation. By using this pipeline, we identified abundant new TIR transposable elements and analyzed their features in maize genomes. These results provided new insight into the impact of TIR elements on maize genome diversity.

To achieve a better application of the pipeline, we upgraded TIR-Learner to a general version so that it can be applied to the genomes other than maize. We conducted a benchmarking project to compare the performance of TIR-Leaner and 10 other programs. In chapter 4, I describe the methods and criteria we used in the benchmarking process and the results based on the performance of each program.

We integrated TIR-Learner into a comprehensive TE annotator called EDTA (Extensive de-novo TE Annotator). In chapter 5, I provide a tutorial of the EDTA pipeline using the rice genome as an example. The results showed that EDTA is a powerful and efficient tool. These pipelines will provide us a better annotation to facilitate future TE research.

In conclusion, this thesis uses both molecular experiments and bioinformatics analysis to uncover the impact of TIR transposable elements on plant genomes. This study will provide new insights into the nature of TEs as well as their relationships with the host genome.