Abstract
Transposable elements (TEs) are often considered as selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. In populations that no longer reproduce sexually, however, the long-term fate of TEs and their hosts is unclear. One possibility is that an asexual lineage may eventually rid itself of deleterious TEs, via increased selection for removal or domestication. Alternatively, TEs may proliferate unabated until the host is driven extinct. Here, we test these ideas using whole-genome sequencing of 26 single individuals from eight species of bdelloid rotifers, a class of invertebrate animals in which males are thus far unknown. We find that all species encode diverse class I retrotransposons and class II DNA transposons, with evidence for recent and ongoing activity. Bdelloid TE content does not appear unusual or deficient when compared to the variation observed in sexual rotifers or other animals. While theory predicts that vertically transmitted class I retrotransposable elements specifically should be scarce after millions of generations of presumed asexuality, we find them in all bdelloid genomes, at lower levels than in sexual relatives, but not so low as to be unprecedented among metazoans more broadly. We consider several possible explanations for these observations. We find no evidence for the hypotheses that cryptic recombination affects TE dynamics in bdelloids, or that TE activity is restrained by unusual adaptations for DNA repair in bdelloid species that tolerate extended desiccation. However, we find that bdelloid genomes share a large expansion and diversification of the Argonaute and RNA-dependent RNA polymerase (RdRP) gene families, which both function in RNAi-mediated TE suppression in other eukaryotes. Indeed, bdelloids may encode the largest expansion of RdRP genes among any eukaryote investigated so far. Thus, it is possible that the deleterious effects of active TEs are mitigated by enhanced cellular defence mechanisms in bdelloids, which might help to compensate for the consequences of long-term asexuality and lateral influx of new TEs.
Competing Interest Statement
The authors have declared no competing interest.