| Summary: | Eukaryotic genomes typically consist of a substantial proportion of repetitive DNA in the form of transposable elements (TEs) and satellite DNA. From studies of mammals, model species, and a few other well studied lineages it is clear that repetitive elements play roles in many important cellular processes and shape evolution of genomes and organisms. However, little is still known about the role of repetitive DNA in biology and genome evolution for most eukaryotic species. Here we use a suite of omics data and genomics analyses to ask the question: What is the role of repeat DNA in genome regulation and structural variation in the Atlantic salmon genome? In papers 1 and 2 we studied the link between evolution of gene regulation and transposable elements in the context of the salmonid whole genome duplication. We found that gene duplicate copies that had evolved lower gene expression across most tissues had increased TE insertion rates in the promoters. In addition, we found that duplicate copies evolving liver specific increase in gene expression, had gained transcription factor binding sites (TFBS) for liver-specific transcription factors in the promoters, and some of these were found inside TEs. In depth analyses of cis-regulatory elements (CREs) in Paper 2 showed that 15-20% of CRE are within TEs (TE-CREs) and that there were fewer TE-CREs active in brain tissue compared to liver. Interestingly, a small heterogeneous group of TE subfamilies (11%) had contributed ~45% of all TE-CREs, but the ‘superspreader’ activity did not seem to peak in the time shortly following the WGD. CREs donated by ‘superspreaders’ were enriched for many different TFBSs, however, highly brain specific TFBSs were extremely rare in TEs, indicating that strong purifying selection shape TE-CRE evolution. In Paper 3 we studied the role of repeat-DNA in the evolution of structural genomic variation (SVs) (>50bp). Leveraging seven new long read genome assemblies we find a large number of so far unknown structural variants, and conclude ...
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