Fig. 3. Summary of the transposable element display method. Genomic DNA is digested with a restriction enzyme (RE) that results in a junction fragment, including the terminal sequences of the element and flanking genomic DNA. Specific adapters are added followed by two rounds of PCR. The first PCR results in the preliminary amplification of the junction fragment, and the second reaction further amplifies the fragments of interest using an element-specific primer labeled with Cy5. Fragments are size fractionated by denaturing acrylamide gel electrophoresis and visualized in a phosphoimager. Each band represents a unique junction fragment. Band intensity reflects template abundance. The most abundant products (darkest bands) are from elements that were inherited vertically, while lighter bands are elements transposing in the somatic tissue of the insect, resulting in clones of cells with the element in a new location. Template abundance of somatic transposition events varies depending on the point in development when transposition occurs. Samples 1-3 represent three Drosophila melanogaster individuals with different genotypes with respect to the location of the autonomous Hermes element inherited through the germ line (arrowheads).