LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

Abstract

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 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 long terminal repeat (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.

FIG. 1.—

Summary of nuclear genome sizes for 13 vertebrate clades. Data are compiled from the Animal Genome Size Database (Gregory 2011). Sample sizes (number of species summarized) are in parentheses following clade names.

FIG. 2.—

The structures of seven full-length TE sequences mined from salamander shotgun reads. Abbreviations: gag, capsid-like protein; pro, protease; RT, reverse transcriptase; rve, integrase; ENV, envelope protein; YR, tyrosine recombinase; EN, endonuclease.

FIG. 3.—

The TE landscape of the Aneides flavipunctatus genome. Element superfamilies are ranked from most to least abundant along the x axis.

FIG. 4.—

The TE landscape of salamanders compared with that of other vertebrates. Salamanders have higher relative levels of LTR retrotransposons. For Danio rerio, we did not include the 11% of the genome identified as repetitive, but classified only as “DNA.”

FIG. 5.—

PCA results summarizing differences in TE landscape across four species. Phylogenetic relationships are (Batrachoseps nigriventris, Eurycea tynerensis), (Aneides flavipunctatus, Desmognathus ochrophaeus).

FIG. 6.—

Age distribution of Ty3/gypsy elements in four species of salamanders.