Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms. Instead, we find that that TE content evolves relatively slowly in bdelloids and that gene families involved in RNAi-mediated TE suppression have undergone significant expansion, which might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

TEs and other repeats were identified using the RepeatModeler and RepeatMasker pipelines. For each sample, a de novo repeat library was generated directly from the assembled nucleotides using RepeatModeler2 (Flynn et al., 2020) and combined with a database of 12,662 protostome repeats from Repbase v23.08 (Bao et al., 2015) and 278 additional TEs manually curated from the A. vaga genome (Flot et al., 2013). Repeats and TEs were then detected and classified using RepeatMasker v4.1.0 (Smit et al., 2013).