In recent years, transposable elements (TEs) have emerged as key factors affecting genome regulation. A pressing challenge now is to understand the biological consequences of TEs reshaping the genome: how important are TEs as sources of adaptive innovations, and what are the long-term implications of TE-activity in eukaryote evolution?
To answer these questions we need to (i) construct highly contiguous genome assemblies that fully incorporate repetitive TEs and (ii) use computational and experimental approaches to evaluate adaptive biological effects of TE-derived evolutionary innovations. Excitingly, with the evolution of single-molecule long-read sequencing, novel computational methods to distinguish adaptive and neutral innovations in genome regulation, and the opportunities CRISPR/Cas9 brings for functional validation, these past challenges and limitations can now be addressed. In TRANSPOSE we will explore how TEs have shaped 1) rediploidization following the salmonid whole genome duplication, 2) remodeling of gene expression evolution, 3) micro-rearrangements and local adaptation, and 4) the evolution of dynamic sex chromosome systems.