The impact of transposable elements on amniote evolution

Transposable elements (TEs) are mobile DNA sequences, often called “jumping genes” because of their ability to replicate to new genomic locations. As a result, TEs make up a significant proportion of the eukaryotic genomes we see today. Growing evidence suggests that TEs are catalysts of genomic change. TE insertions into regulatory regions can lead to new genes, or they can disrupt host sequences and serve as substrates for homologous recombination, generating DNA rearrangements. At the RNA level, TEs can carry transcription factor binding sites, causing alternative splicing and thus impacting gene expression. Some TEs are even capable of jumping between different genomes, using viruses or parasitic insects as transfer vectors. Originally viewed as “junk” DNA, TEs are now recognised as powerful drivers of genome evolution. However, there are numerous computational challenges to accurately detecting and characterising TEs in genomic data. Many existing tools and pipelines are designed to explicitly remove repetitive, non-unique sequences. Likewise, TE annotation software relies heavily on the use of query sequences and reference databases. This restricts the ability to find new types of TEs (or mutated forms of known TEs), mainly suited to the analysis of model organisms such as human and mouse. In this thesis, I describe an ab initio pipeline for identifying species-specific repeats and segmental duplications with high sensitivity and accuracy. I consider a repeat in the truest sense of the word: any sequence that appears more than once in the genome. Using eight representative species from each branch of amniote evolution, I use this novel method to portray the remarkable diversity of TEs across species and trace different repeats to their families and consensus sequences. Reptiles are particularly renowned for their unusual TE dynamics. In Chapter 3, I investigate TE evolution in the tuatara genome: a New Zealand reptile. The tuatara is the only surviving member of its order, which flourished around 200 million years ago. Its most recent common ancestor with any other extant group is the lizards and snakes. The tuatara is therefore of great interest to evolutionary geneticists. In most reptiles, CR1 repeats make up the dominant TE class. My results indicate that the tuatara genome is distinct from other reptiles because the two most dominant TE families are L2 and MIR elements. Furthermore, I describe a likely transfer of L2 elements between tuatara and monotremes (platypus and echidna), potentially explaining the predominance of L2s in the tuatara genome. In Chapter 4, I extend my TE analysis to consider gene expression in six species. Due to the prevalence of TEs in the genome, I used a bootstrap approach to minimize the co-occurrence of multiple TE types in one gene. My results show that species-specific associations of TEs with gene expression support a role for TEs in speciation/response to selection by species. Altogether, this thesis presents novel and ab initio approaches for identifying and annotating repetitive elements. By characterizing millions of repeats across different amniote species, and investigating their association with gene expression, I provide evidence for their impact and importance in amniote evolution.Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Biological Sciences, 201