Identification of a “new” <i>crystal/Su(Ste)</i> locus on the <i>Drosophila melanogaster</i> Y chromosome, resembling a piRNA cluster regulating <i>Stellate</i> repeats and transposons

The crystal-Stellate interaction is the first known example of piRNA-mediated regulation between heterochromatin (the crystal/Suppressor of Stellate [Su(Ste)] locus on the Y chromosome) and euchromatin (the Stellate locus on the X chromosome) in Drosophila melanogaster. Here, we comprehensively annotate the Y-linked crystal/Su(Ste) sequences using Release 6 and heterochromatin-enriched scaffolds and contigs. In Release 6, we mapped two distinct crystal/Su(Ste) repeat regions with different molecular organizations. Beyond the ordered, tandem "classical" region, we identified a novel, disorganized region containing sequence fragments in both orientations derived from both crystal/Su(Ste) repeats and transposable elements. This disorganized locus displays structural features of a piRNA cluster that regulates both Stellate repeats and transposons. Furthermore, we identified at least four additional loci with organized crystal/Su(Ste)-like repeats within heterochromatin-enriched sequences not included in Release 6. We also conducted a detailed examination of the complex relationship between Release 6 sequences and more recent scaffolds and contigs. Alongside the classic crystal/Su(Ste) repeat containing hoppel/1360 fragments, we discovered two new repeat types structurally organized like crystal/Su(Ste) but carrying portions of HetA and gypsy12 transposons. Overall, these findings provide structural insights into the crystal-Stellate system, refining the Drosophila melanogaster Y chromosome map.