Template switching can create complex LTR retrotransposon insertions in Triticeae genomes

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.Those complex elements are part of the genome structure of plants in the Poaceae, especially in the Triticeae, but not of Arabidopsis. Hence, retrotransposon dynamics shaping the genome are lineage-specific.Long Terminal Repeat (LTR) retrotransposons are Class I transposable elements that replicate by a "Copy-and-Paste" mechanism, called retrotransposition, which is quite similar to lentivirus (such as the HIV) replication. Higher plant genomes, especially of the grasses (such as maize, wheat and barley), harbor a large number of these elements, which form the vast majority of the nuclear DNA. Retrotransposition involves a reverse transcription step, where cDNA is synthesized from an RNA template. Reverse transcription is catalyzed by reverse transcriptase, which is generally encoded by the retrotransposon being copied, and the cDNA is inserted into a new genomic location by the integrase, which is also self-encoded [1]. A canonical retrotransposon insertion comprises two LTRs and an internal domain containing the coding domain for integrase, reverse transcriptase, a proteinase, the structural protein GAG, and the signals for reverse transcription.Many composite structural patterns derived from canonical LTR retrotransposon insertions were previously identified in BACs and others long genomic sequences from various plants (Figure 1; [2-7] and references within). These appear primarily as nested insertions of one retroelement into another. The nests can comprise more than three or four layers arranged in a "Russian doll" fashion. In some cases, the nested retroelements are solo LTRs rather than elements containing two LTRs and a central domain. The solo LTRs