Evolutionary and epigenetic interaction between transposable elements and their plant hosts

My thesis sought to investigate the epigenetic and evolutionary interactions between various transposable elements (TEs) and their plant hosts. All analyses were conducted by utilising bioinformatic approaches, which include programming languages and biological software. In the first chapter of my thesis, the ATHILAfinder tool is described, which is a pipeline for the large-scale and accurate discovery of ATHILA elements in sequenced genomes. This is a novel tool, because the ATHILA clade of transposable elements has colonised all branches of the plant tree of life and they are exhibiting a predilection for integration in Arabidopsis centromeres which alters the centromeric morphology (see second chapter). Furthermore, the availability of pipelines tailored for specific TE types like ATHILA elements is limited, but they can significantly improve TE identification and, hence empower downstream analysis, by providing high quality elements. The second chapter examines, phylogenetically and with regard to the location on chromosomes, the ATHILA elements that were found in several Arabidopsis assemblies of the species Arabidopsis thaliana and Arabidopsis lyrata. As a result of some ATHILA families' preference to integrate into the centromeres, the centromeric architecture is changed. This alteration is taking place through rapid cycles of transposon invasion and purging of them via satellite homogenisation, which drive centromere evolution and may ultimately contribute to speciation. Finally, the third chapter attempts to decode the cis-regulatory region of various LTR retrotransposon families. These regions are important as they control when and where the TEs will activate and they may also be a prime target of host defences as methylating these regions can suppress TE activity. Additionally, our knowledge about them is limited. Our results show that cisregulatory regions are complex. They are characterised by a large number of palindromic motifs that form stable secondary structures and the areas around them are hotspots of recombination. In addition, LTR retrotransposons that predate the split between closely related species now contain different palindromes which indicates rapid evolution of these sequences. These thesis' findings shed light on a small portion of the intriguing world of transposable elements in plants.</p

Evolutionary and epigenetic interaction between transposable elements and their plant hosts

My thesis sought to investigate the epigenetic and evolutionary interactions between various transposable elements (TEs) and their plant hosts. All analyses were conducted by utilising bioinformatic approaches, which include programming languages and biological software. In the first chapter of my thesis, the ATHILAfinder tool is described, which is a pipeline for the large-scale and accurate discovery of ATHILA elements in sequenced genomes. This is a novel tool, because the ATHILA clade of transposable elements has colonised all branches of the plant tree of life and they are exhibiting a predilection for integration in Arabidopsis centromeres which alters the centromeric morphology (see second chapter). Furthermore, the availability of pipelines tailored for specific TE types like ATHILA elements is limited, but they can significantly improve TE identification and, hence empower downstream analysis, by providing high quality elements. The second chapter examines, phylogenetically and with regard to the location on chromosomes, the ATHILA elements that were found in several Arabidopsis assemblies of the species Arabidopsis thaliana and Arabidopsis lyrata. As a result of some ATHILA families' preference to integrate into the centromeres, the centromeric architecture is changed. This alteration is taking place through rapid cycles of transposon invasion and purging of them via satellite homogenisation, which drive centromere evolution and may ultimately contribute to speciation. Finally, the third chapter attempts to decode the cis-regulatory region of various LTR retrotransposon families. These regions are important as they control when and where the TEs will activate and they may also be a prime target of host defences as methylating these regions can suppress TE activity. Additionally, our knowledge about them is limited. Our results show that cisregulatory regions are complex. They are characterised by a large number of palindromic motifs that form stable secondary structures and the areas around them are hotspots of recombination. In addition, LTR retrotransposons that predate the split between closely related species now contain different palindromes which indicates rapid evolution of these sequences. These thesis' findings shed light on a small portion of the intriguing world of transposable elements in plants.</p

Cycles of satellite and transposon evolution in Arabidopsis centromeres

Centromeres are critical for cell division, loading CENH3 or CENPA histone variant nucleosomes, directing kinetochore formation and allowing chromosome segregation1,2. Despite their conserved function, centromere size and structure are diverse across species. To understand this centromere paradox3,4, it is necessary to know how centromeric diversity is generated and whether it reflects ancient trans-species variation or, instead, rapid post-speciation divergence. To address these questions, we assembled 346 centromeres from 66 Arabidopsis thaliana and 2 Arabidopsis lyrata accessions, which exhibited a remarkable degree of intra- and inter-species diversity. A. thaliana centromere repeat arrays are embedded in linkage blocks, despite ongoing internal satellite turnover, consistent with roles for unidirectional gene conversion or unequal crossover between sister chromatids in sequence diversification. Additionally, centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, in line with cycles of repeat evolution. Centromeric sequence changes are even more extreme in comparison between A. thaliana and A. lyrata. Together, our findings identify rapid cycles of transposon invasion and purging through satellite homogenization, which drive centromere evolution and ultimately contribute to speciation