Targeted identification of TE insertions in a Drosophila genome through hemi-specific PCR.

Transposable elements (TEs) are major components of eukaryotic genomes and drivers of genome evolution, producing intraspecific polymorphism and interspecific differences through mobilization and non-homologous recombination. TE insertion sites are often highly variable within species, creating a need for targeted genome re-sequencing (TGS) methods to identify TE insertion sites. Here, we adapt a hemi-specific PCR approach for TGS of P-elements in Drosophila genomes on the Illumina platform. By comparing our results to TE annotations based on whole genome re-sequencing (WGS) data for the same Drosophila melanogaster strain, we demonstrate that TGS is powerful for identifying true insertions, even in repeat-rich heterochromatic regions. TGS also provides precise genomic positions for all annotated TE insertions.