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Genomic dynamics of transposable elements in the Western clawed frog (Silurana tropicalis)


Chain,  Frédéric J. J.
Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Shen, J. J., Dushoff, J., Bewick, A. J., Chain, F. J. J., & Evans, B. J. (2013). Genomic dynamics of transposable elements in the Western clawed frog (Silurana tropicalis). Genome biology and evolution, 5(5), 998-1009. doi:10.1093/gbe/evt065.

Transposable elements (TEs) are repetitive DNA sequences that canmake new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation,weevaluated correlations between several genomic variables and the presence of TEs and non-TE repeats inthecompletegenomesequenceof theWesternclawedfrog (Siluranatropicalis). This analysis revealspatternsof TEinsertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of longterminal repeat (LTR) andnon-LTR retrotransposons were fixed at only 4of16sites and at lowfrequency at 12of 16. Amaximumlikelihoodmodelfailed toattribute thesedifferences in insertion frequencies tovariation inselection pressureondifferent classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.