Transposable element diversity and activity patterns in neotropical salamanders

Transposable elements (TEs) compose a substantial proportion of the largest eukaryotic genomes. TE diversity has been hypothesized to be negatively correlated with genome size, yet empirical demonstrations of such a relationship in a phylogenetic context are largely lacking. Furthermore, the most abundant type of TEs in genomes varies across groups, and it is not clear if there are patterns of TE activity consistent with genome size among different taxa with large genome sizes. We use low-coverage sequencing of 16 species of Neotropical salamanders, which vary approximately seven-fold in genome size, to estimate TE relative abundance and diversity for each species. We also compare divergence of copies of each TE superfamily to estimate patterns of TE activity in each species. We find a negative relationship between TE diversity and genome size, which is consistent with the hypothesis that either competition among TEs or reduced selection against ectopic recombination may result in lower diversity in the largest genomes. We also find divergent activity patterns in the largest vs. the smallest genomes, suggesting that the history of TE activity may explain differences in genome size. Our results suggest that both TE diversity and relative abundance may be predictable, at least within taxonomic groups.

Methods
Low coverage sequencing genomic libraries were prepared and sequenced at the Vincent J. Coates Sequencing facility, QB3, at the University of California, Berkley, using the NovaSeq S4 seqquencing platform. Four samples were selected to asse,ble draft contigs using dipSPADES (Safanova et al. 2015). Transposable elements were retrieved and annotated using PiRATE (Pipeline to Retrieve and Annotate Transposable Elements).