Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris

Octopuses are phenotypically distinctive organisms, and recent genomic work raises questions about the contributions of transposable elements (TEs) to their genomic architecture. We leveraged a robust repeat annotation pipeline, in combination with manual and automated curatorial techniques, to produce a more comprehensive repeat annotation of Octopus vulgaris. This revealed that ∼66% of the genome are repeats, in contrast to previous estimates of 43% to 50% in closely related octopus species. Whereas previous studies of TE expansion in Octopus bimaculoides identified two bursts of activity, 25 and 56 MYA, our re-annotation revealed four such expansions at 18, 25, 33, and 56 MYA. We further identified a landscape of TE hot- and cold spots. This refined TE timescape and landscape will serve as a useful basis for understanding TE contributions to O. vulgaris evolution, also for identifying factors contributing to variation in the TE community across genomic space and evolutionary time.