GENomes Evolve in a Landscape of TEs

forthcoming

Understanding how genomes work is intimately entangled with understanding how they evolved. Although most individual mutations are single-base, more sequence is changed through structural variation, which itself is in large part driven by transposable elements (TEs), frequently with greater functional and reproductive consequences. Here we will take a multi-pronged and interdisciplinary approach to advance our understanding of how the genomes of multicellular eukaryotes and their TEs co-evolve, building on the near-perfect genome assemblies arriving at an exponentially increasing rate from long-read technologies. We will develop new efficient computational tools that operate at the scale of the data that is coming, and couple them to powerful population genetic, phylogenetic and experimental approaches to study the dynamics of TE invasions in Arabidopsis and Drosophila, the preeminent systems for genetic analysis of TE-host interactions. We will extend “ancestral recombination graph” approaches beyond current models of point mutation and homologous recombination to also support transposition, non-homologous recombination and other forms of structural rearrangement - this will properly account for these processes in a powerful framework for analysis of selection, population history and trait association. We will then apply these tools to two vertebrate systems, the Malawi cichlid fish radiation and the bats, in both of which increased TE activity is seen alongside rapid evolution with remarkable adaptations to phenotype and lifestyle, and will collaborate with others including those generating large Tree of Life genome datasets. The resulting advances will connect top-down genomic sequence analysis with bottom-up mechanistic studies of TE function, via population-genetic analysis of demography and selection. This will support the development of a new framework, methodology and understanding of genome sequence variation and genome evolution in all its variety.