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MBE Advance Access published online on September 21, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm197
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Population and Evolutionary Dynamics of Helitron Transposable Elements in Arabidopsis thaliana

Jesse D. Hollister and Brandon S. Gaut1

Department of Ecology and Evolutionary Biology, U.C. Irvine, Irvine, CA 92697-2525

1 Address for Correspondence: Brandon Gaut, 321 Steinhaus Hall, U.C. Irvine, Irvine, CA 92697-2525, bgaut{at}uci.edu, Phone: 949 824-2564, FAX: 949 824-2181

Received for publication April 9, 2007. Revision received August 5, 2007. Accepted for publication August 30, 2007.

Helitrons, a recently discovered super-family of DNA transposons that capture host gene fragments, constitute up to 2% of the Arabidopsis thaliana genome. In this study, we identified 565 insertions of a family of non-autonomous Helitrons, known as Basho elements. We aligned subsets of these elements, estimated their phylogenetic relationships, and used branch lengths to yield insight into the age of each Basho insertion. The age distribution suggests that 87% of Bashos inserted within five million years, subsequent to the divergence between A. thaliana and its sister species A. lyrata. We screened 278 of these insertions for their presence or absence in a sample of 47 A. thaliana accessions. With both phylogenetic and population frequency data, we investigated the effects of gene density, recombination rate, and element length on Basho persistence. Our analyses suggested that longer Basho copies are less likely to persist in the genome, consistent with selection against the deleterious effects of ectopic recombination between Basho elements. Furthermore, we determined that 39% of Basho elements contain fragments of expressed protein-coding genes, but all of these fragments were explained by only five gene capture events. Overall, the picture of A. thaliana Helitron evolution is one of rapid expansion, relatively few gene capture events and weak selection correlated with element length.

Key Words: Helitron • exon shuffling • ectopic recombination


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