Data from: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

Among vertebrates, most of the largest genomes are found within the
salamanders, a clade of amphibians that includes 613 species. Salamander
genome sizes range from ∼14 Gb to ∼120 Gb. Because genome size is
correlated with nucleus and cell sizes, as well as other traits,
morphological evolution in salamanders has been profoundly affected by
genomic gigantism. However, the molecular mechanisms driving genomic
expansion in this clade remain largely unknown. Here, we present the first
comparative analysis of transposable element (TE) content in salamanders.
Using high-throughput sequencing, we generated genomic shotgun data for
six species from the Plethodontidae, the largest family of salamanders. We
then developed a pipeline to mine TE sequences from shotgun data in taxa
with limited genomic resources, such as salamanders. Our summaries of
overall TE abundance and diversity for each species demonstrate that TEs
make up a substantial portion of salamander genomes, and that all of the
major known types of TEs are represented in salamanders. The most abundant
TE superfamilies found in the genomes of our six focal species are
similar, despite substantial variation in genome size. However, our
results demonstrate a major difference between salamanders and other
vertebrates: salamander genomes contain much larger amounts of LTR
retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase
in genome size that occurred in salamanders was likely accompanied by a
shift in TE landscape. These results suggest that increased proliferation
of LTR retrotransposons was a major molecular mechanism contributing to
genomic expansion in salamanders.