Journal of Molecular Evolution

, Volume 83, Issue 3–4, pp 126–136 | Cite as

Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus

  • M. J. Madison-Villar
  • Cheng Sun
  • Nelson C. Lau
  • Matthew L. Settles
  • Rachel Lockridge Mueller
Original Article


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.


Genome size evolution Small RNA evolution Transposable element silencing piRNA-mediated transposon silencing 



This research was supported by NSF–DBI 1103746 to MM-V and NSF-DEB 1021489 to RLM. NCL was supported by the Searle Scholars Foundation and the NIH (R00HD057298). J. Krakovil and D. Weisrock (U Kentucky) provided the tissues and access to unpublished Cryptobranchus alleganiensis transcriptome data; funding for collecting trips was provided by Highlands Biological Station and the University of Kentucky Department of Biology to J. Krakovil. D. New at IBEST provided critical technical expertise. Suggestions from anonymous reviewers improved the quality of the manuscript.

Supplementary material

239_2016_9759_MOESM1_ESM.pdf (484 kb)
Supplementary material 1 (PDF 483 kb) Transposable element families targeted by piRNAs and siRNAs in the female and male samples. Results were obtained from mapping each small RNA dataset to its respective reference transcriptome. TE families are ranked by density of mapped small RNA reads
239_2016_9759_MOESM2_ESM.pdf (1.5 mb)
Supplementary material 2 (PDF 1550 kb) Phylogenies estimated for eleven piRNA pathway protein sequences obtained from salamanders and other vertebrates


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • M. J. Madison-Villar
    • 1
  • Cheng Sun
    • 1
    • 2
  • Nelson C. Lau
    • 3
  • Matthew L. Settles
    • 4
    • 5
  • Rachel Lockridge Mueller
    • 1
  1. 1.Department of BiologyColorado State UniversityFort CollinsUSA
  2. 2.Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural ResearchChinese Academy of Agricultural SciencesBeijingChina
  3. 3.Department of BiologyBrandeis UniversityWalthamUSA
  4. 4.Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowUSA
  5. 5.Bioinformatics CoreUC Davis Genome CenterDavisUSA

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