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Originally published as Genetics Published Articles Ahead of Print on May 23, 2005.
Genetics, Vol. 170, 1081-1089, July 2005, Copyright © 2005
doi:10.1534/genetics.105.042564
Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum
Michael E. Hood*,1,
Melanie Katawczik
and
Tatiana Giraud
* Department of Biology, University of Virginia, Charlottesville, Virginia 22903
Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695
Ecologie, Systématique et Evolution, Université Paris-Sud, F-91405 Orsay Cedex, France
1 Corresponding author: Department of Biology, Gilmer Hall, University of Virginia, Charlottesville, VA 22903.
E-mail: michael.hood{at}virginia.edu
Repeat-induced point mutation (RIP) is a genome defense in fungi that hypermutates repetitive DNA and is suggested to limit the accumulation of transposable elements. The genome of Microbotryum violaceum has a high density of transposable elements compared to other fungi, but there is also evidence of RIP activity. This is the first report of RIP in a basidiomycete and was obtained by sequencing multiple copies of the integrase gene of a copia-type transposable element and the helicase gene of a Helitron-type element. In M. violaceum, the targets for RIP mutations are the cytosine residues of TCG trinucleotide combinations. Although RIP is a linkage-dependent process that tends to increase the variation among repetitive sequences, a chromosome-specific substructuring was observed in the transposable element population. The observed chromosome-specific patterns are not consistent with RIP, but rather suggest an effect of gene conversion, which is also a linkage-dependent process but results in a homogenization of repeated sequences. Particular sequences were found more widely distributed within the genome than expected by chance and may reflect the recently active variants. Therefore, sequence variation of transposable elements in M. violaceum appears to be driven by selection for transposition ability in combination with the context-specific forces of the RIP and gene conversion.
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