Program > Browse abstracts by author > Tolar Nikolas

Aside from their exceptionally long lifespans and resistance to aging-related diseases, female African mole-rats (Rodentia: Bathyergidae) are fertile for most of their life. As transposable elements (TEs) have been previously implicated in aging and inflammatory responses, we would like to explore possible connections between the TE content of African mole-rat oocytes and their unusual reproductive longevity. In this study, we first compared the TE content of three African mole-rat species (naked-mole rat, Mechow's mole-rat and Damara mole-rat) to three other rodent species (mouse, Upper Galilee Mountains blind mole rat and guinea pig) by creating two sets of TE libraries/annotations: one with all TEs using RepeatModeler and RepeatMasker, and another specifically for LTR-retrotransposons (LTR-RTs) using LTR_retriever. We used two genome assemblies for naked mole-rat: its reference genome generated with short-read data, and a newer chromosome-level assembly created with long reads. As in previous studies, we found the number of total and young TE and LTR-RT sequences in African mole-rats to be lower than in mouse. However, we observed a higher number of LTR-RTs and a more recent LTR-RT acquisition peak from the new naked mole-rat assembly compared to the reference genome. We then compared rates of LTR-RT removal through ectopic recombination between mole-rats and other rodents. While Mechow's mole-rat had the highest ratio of solo LTR versus intact LTR-RTs, Damara mole-rat and naked mole-rat had the lowest and second lowest, respectively. Our results suggest that although African mole-rats have relatively fewer total and young TE insertions, recombination-based LTR-retrotransposon removal is not conserved in African mole-rats and cannot fully explain their low LTR-RT content. Furthermore, reported TE content and age can vary depending on the quality of the genome assembly and the TE detection method used.