Two of the most potent drivers of genome evolution in eukaryotes are whole genome duplications (WGD) and transposable element (TE) activity. These two mutational forces can also play synergistic roles; WGDs result in both cellular stress and functional redundancy, which would allow TEs to escape host-silencing mechanisms and effectively spread with reduced impact on fitness. As TEs can function as, or evolve into, TE-derived cis-regulatory elements (TE-CREs), bursts of TE-activity following WGD are likely to impact evolution of gene regulation. However, the role of TEs in genome regulatory remodelling after WGDs is unclear. Here we used the salmonids, known to have experienced massive expansion of TEs after a WGD ∼100 Mya, as a model system to explore the synergistic role of TEs and WGDs on genome regulatory evolution.
Our results do not support a WGD-associated TE-CRE rewiring of gene regulation. Instead we find that TEs from diverse superfamilies have been particularly effective in spreading TE-CREs and shaping gene regulatory networks under tissue-specific selection pressures, across millions of years following the salmonid WGD.