Transposable elements (TEs) are abundant, mobile DNA sequences whose behavior can have profound evolutionary impacts. Recent research has shown that they can modify gene regulation and drive structural rearrangements of chromosomes. Despite half a century of investigation, fundamental questions remain unanswered about the evolutionary consequences of TE activity, the evolutionary forces determining the distribution of TEs across taxa, and the frequency with which TEs are co-opted by natural selection to increase fitness and create adaptive innovations.

Salmonid fishes are an excellent model system with which to explore the role of TEs in genome evolution and the creation of adaptive innovations. Species vary with respect to the quantity and diversity of TEs, and interspecies comparisons will reveal how different families of TEs reshape genomes and gene regulatory networks over time. In addition, these fishes have undergone adaptive divergence and radiation following a recent whole genome duplication event, enabling us to explore mechanistic links between TEs and genomic architecture. Finally, salmonids have a novel sex chromosome system with a jumping TE-encapsulated male determiner in Atlantic salmon, making them a good model to better understand the link between sex chromosome evolution in the resolution of sexual conflict.

In TRANSPOSE, we will use new long-read sequencing technology to generate highly contiguous genome assemblies of 11 salmonid lineages, allowing for more detailed and comprehensive mapping of TEs.  We will combine these improved genome sequences with functional genomics and novel phylogenetics methods to enhance our understanding of the role of TEs in adaptation and the evolution of genomes and gene regulation.