Journal Article

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

Cheng Sun, Donald B. Shepard, Rebecca A. Chong, José López Arriaza, Kathryn Hall, Todd A. Castoe, Cédric Feschotte, David D. Pollock and Rachel Lockridge Mueller

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 4, issue 2, pages 168-183
Published in print January 2012 |
Published online December 2011 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evr139

More Like This

Show all results sharing these subjects:

  • Bioinformatics and Computational Biology
  • Evolutionary Biology
  • Genetics and Genomics

GO

Show Summary Details

Preview

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.

Keywords: LTR retrotransposon; transposable element landscape; genomic expansion; TE age distributions; genome size evolution; plethodontid salamanders

Journal Article.  9078 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.