Extensive tandem repeat repertoires in ranid frogs and the role of transposable elements in their evolution

Abstract

Tandem repeats (satellite DNA) are prevalent in eukaryotic genomes and contribute to chromosome organization and genome evolution. Amphibians possess unusually large, repeat-rich genomes and therefore provide a valuable system for investigating the origin, diversity, and genomic dynamics of tandem repeats. Despite this, comparative analyses of tandem repeat repertoires in amphibians remain limited. A genome-wide analysis of tandem repeats in nine species of true frogs from the family Ranidae showed that tandem repeat content is exceptionally high and positively correlated with genome size. Comparative analyses revealed a hierarchical organization of tandem repeat families, that range from widely conserved families to lineage-restricted and species-specific repeats. A prominent feature of these genomes is the high proportion of tandem repeats with sequence homology to transposable elements; such repeats account for 43–91% of the total tandem repeat length and correlate with both genome size and overall tandem repeat content. In silico analyses indicated broad chromosomal distribution of tandem repeats. Fluorescence in situ hybridization confirmed that tandem repeats that are homologous to transposable elements, as well as those that are not, are widely dispersed and occupy pericentromeric, subtelomeric and interstitial regions. Ranidae genomes contain extensive tandem repeat repertoires. These repeats are broadly distributed along chromosomes. The coexistence of conserved and lineage-restricted tandem repeat families with transposable element homology suggests recurrent involvement of transposable elements in the emergence of new tandem repeats. These findings indicate that the evolutionary dynamic of amphibian genomes is associated with sustained accumulation and expansion of tandem repeats.