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Original article (peer-reviewed)

Journal The Plant Journal
Title of proceedings The Plant Journal
DOI 10.1111/j.1365-313X.2012.05007.x

Abstract

Intergenic sequences evolve rapidly in plant genomes through a process known as genomic turnover. To investigate the influence of DNA transposons on genomic turnover, we compared 1 Mbp of orthologous genomic sequences from Brachypodium distachyon and Brachypodium sylvaticum. We found that B. distachyon and B. sylvaticum diverged approximately 1.7–2.0 million years ago. Out of a total of 219 genes identified on the analyzed sequences, 211 were colinear. In contrast, only 24 transposable elements (TEs) out of a total of 451 were orthologous (i.e. inserted in the common ancestor). We could characterize in detail 59 insertions and 60 excisions of DNA transposons in one or the other species which exchanged 17% of the intergenic space. DNA transposon excision sites showed complex and highly diagnostic sequence motifs of double strand break (DSB) repair. This indicates that DNA transposon excisions can lead to extensive deletions of hundreds of bp of flanking sequence if the DSB is repaired by “Single Strand Annealing”, or to insertions of up to several hundred bp of “filler DNA” if the DSB is repaired by “Synthesis Dependent Strand Annealing”. In some cases, DSBs were repaired by a combination of both. We present a model for the evolution of intergenic sequences in which repair of DSBs upon DNA transposon excision is a major factor in the rapid turnover and erosion of intergenic sequences.© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd
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