| Summary: | <p>Abstract</p> <p>Background</p> <p>The LTR (long terminal repeat) retrotransposons of higher plants are replicated by a mutagenic life cycle containing transcription and reverse transcription steps. The DNA copies are often subject to recombination once integrated into the genome. Complex elements, where two elements share an LTR, are not uncommon. They are thought to result from heterologous recombination between two adjacent elements that occurs following their integration.</p> <p>Results</p> <p>Here, we present evidence for another potential mechanism for the creation of complex elements, involving abnormal template switching during reverse transcription. The template switching creates a large, complex daughter element, formed by the fusion of two parent sequences, which is then inserted into the genome.</p> <p>Conclusion</p> <p>Those complex elements are part of the genome structure of plants in the <it>Poaceae</it>, especially in the Triticeae, but not of <it>Arabidopsis</it>. Hence, retrotransposon dynamics shaping the genome are lineage-specific.</p>
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