A reference genome for cultured Drosophila ovarian somatic cells enables studies of transposon and piRNA biology

Background Accurate reconstruction of repetitive genomic regions is essential to understand small RNA–mediated transposon silencing. In Drosophila ovarian somatic cells (OSCs), a primary model for nuclear PIWI–piRNA biology, reliance on the D. melanogaster reference (dm6) obscures cell-line–specific transposon insertions and the architecture of piRNA source loci. Results We generated a highly contiguous de novo assembly of the OSC genome that reveals a transposon landscape diverging substantially from dm6. The assembly fully resolves the ∼700 kb flamenco locus, the principal piRNA cluster in OSCs, and yields a genome-wide map of transposon insertions. By integrating this assembly with functional genomics datasets, we define OSC piRNA source loci, show that cluster sequence composition determines transposon piRNA output, and demonstrate the widespread effects of Piwi on heterochromatin formation. Conclusions The OSC assembly establishes a precise genomic framework for interpreting piRNA and chromatin data in this model system. To enable community use of this resource for studies of transposon control and piRNA biology, we provide an integrated genome browser and data-sharing platform.