Abstract: Genomes have a highly organised architecture (non-random organisation of functional and non-functional genetic elements within chromosomes) that is essential for many biological functions, particularly, gene expression and reproduction. However, despite the need to conserve genome architecture, a surprisingly high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. Within plant genomes, the processes of genome architecture divergence are not well described. During my PhD, I investigated genome architecture conservation and divergence in wildEucalyptus species using long-read sequencing and de novo assembly. By analysing the genomes of 33 phylogenetically diverse Eucalyptus species, covering 1-50 million years of diverging genome evolution. We measured genome architectural conservation and divergence, describing the pattern of genome evolution among these species. The results revealed that immediately following lineage divergence, genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and subsequent divergence beyond recognition of rearrangements becomes the primary driver of genome divergence. The loss of syntenic regions (a region that retains ancestral/shared genome architecture) also contributes to genome divergence but at a slower pace than rearrangements. Further examination of identified rearrangements suggests that rearrangements may be altering the phenotypes of Eucalyptus species. The primary mechanism of genome rearrangement is unequal homologous recombination, which is more likely to occur within genome regions that contain highly similar sequences such as transposons. The examination of three closely related Eucalyptus genomes further demonstrates that rearrangements often occur within transposon-rich regions, suggesting that transposons contribute to genome fragmentation. This work also emphasises that the use of single reference genomes in genomic variation studies could lead to reference bias, especially when examining potentially adaptive loci that have significantly diverged, been deleted, duplicated, or rearranged. Finally, we provide an unbiased framework for investigating potential speciation and adaptive loci among a rapidly radiating foundation species of woodland trees that are free from selective breeding seen in most crop species.

Biography: Leaving an unfulfilling job, Scott came to university later in life. Inspired by the advances in biology and the surrounding media coverage he studied biology. In 2019 he graduated from the ANU with a Bachelor of Science (Honours). He continued his honours work within the Borevitz lab and began his Ph.D. in 2020. His research focuses on studying genome evolution, using the Eucalyptus genus of trees.