Whether you consider them major genomic parasites or potentially major drivers of genome expansion, long terminal repeat (LTR) retrotransposons are major, making up 15 to 90% of plant nuclear genomes (reviewed in Sabot and Schulman, 2006). These elements transpose by a replicate-and-paste mechanism, wherein an RNA copy of the retrotransposon is reverse transcribed into DNA, which then integrates into the host genome at a new location. This requires a set of proteins, including reverse transcriptase and integrase, encoded by autonomous retrotransposons. LTR retrotransposons that do not have the suite of required proteins are generally referred to as nonautonomous; many of the nonautonomous elements are dead, but some can make new copies by exploiting the proteins produced by their autonomous partners. The evolution and maintenance of the relationships among autonomous elements and their nonautonomous counterparts have proven to be complex and intriguing. For example, how do nonautonomous elements maintain sequence conservation in cis-sequences required for transposition, including the LTRs, the primer binding site, the