Data from: Small RNAs from a big genome: the piRNA pathway and transposable elements in the salamander species Desmognathus fuscus
Madison-Villar, Mercedita J., Colorado State University
Sun, Cheng, Colorado State University
Lau, Nelson C., Brandeis University
Settles, Matthew L., University of Idaho
Mueller, Rachel Lockridge, Colorado State University
Published Sep 06, 2017 on Dryad.
Cite this dataset
Madison-Villar, Mercedita J. et al. (2017). Data from: Small RNAs from a big genome: the piRNA pathway and transposable elements in the salamander species Desmognathus fuscus [Dataset]. Dryad. https://doi.org/10.5061/dryad.kv57r
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules. In most known animals, TE activity in the germline is primarily regulated by the Piwi-interacting RNA (piRNA) pathway. In this study, we test the hypothesis that salamanders’ unusually high TE loads reflect the loss of the ancestral piRNA-mediated TE-silencing machinery. We characterized the small RNA pool in the female and male adult gonads, testing for the presence of small RNA molecules that bear the characteristics of TE-targeting piRNAs. We also analyzed the amino acid sequences of piRNA pathway proteins from salamanders and other vertebrates, testing whether the overall patterns of sequence divergence are consistent with conserved pathway function across the vertebrate clade. Our results do not support the hypothesis of piRNA pathway loss; instead, they suggest that the piRNA pathway is expressed in salamanders. Given these results, we propose hypotheses to explain how the extraordinary TE loads in salamander genomes could have accumulated, despite the expression of TE-silencing machinery.
Nexus file containing the trimmed alignment of amino acid sequences from salamanders and other vertebrates used to generate the phylogeny in the manuscript.
Cryptobranchus pRNA proteins
Amino acid sequences for the 12 Cryptobranchus alleganiensis piRNA pathway proteins.
National Science Foundation, Award: NSF-DEB 1021489