Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats

The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, usually around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian genomes also exhibit a precipitous decline in Class II activity beginning roughly 40 million years ago (Ma). The first signs of more recently active mammalian Class II TEs were obtained from the little brown bat, Myotis lucifugus and are reflected by higher genome content (~5%). To aid in determining taxonomic limits and potential impacts of this elevated Class II activity, we performed 454 survey sequencing of a second Myotis species as well as four additional taxa within the family Vespertilionidae and an outgroup species from Phyllostomidae. Graph-based clustering methods were used to reconstruct the major repeat families present in each species and novel elements were identified in several taxa. Retrotran...