Transposable elements in the salmonid genome




Minkley, David Richard

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Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs.



Transposable elements, Salmon, Genome annotation, Repeats, Genome evolution, Bioinformatics, Speciation, Evolution, Tc1-Mariner, Whole genome duplication, Polyploidy, Fish, Rainbow trout, Arctic char, Atlantic salmon, Coho salmon, Chinook salmon, Salmo salar, Salvelinus alpinus, Oncorhynchus mykiss, Oncorhynchus kisutch, Oncorhynchus tshawytscha