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[Preprint]. 2026 Jan 21:2026.01.18.700156. [Version 1] doi: 10.64898/2026.01.18.700156

Figure 2: Synteny between Iso1 and its sublines reveals simple deletions.

Figure 2:

The colored karyoplot shows the detailed structure of the genomic region containing the Rsp locus in the parent strain Iso1 (total Rsp copy number 1756), and its allelic deletion series: Iso1ΔC8 (total Rsp copy number 851), Iso1ΔC16 (total Rsp copy number 812), and Iso1ΔC16Δ20 (total Rsp copy number 211). In each subline, Rsp is flanked proximally by the simple satellite AAGAG and distally by TE clusters, most notably, the Bari1 cluster. The shaded blocks between subline alleles indicate regions of pairwise synteny with Iso1: yellow blocks for Iso1 and Iso1ΔC8; blue blocks for Iso1 and Iso1ΔC16, and grey blocks for Iso1 and Iso1ΔC16Δ20. In each case, the deletions appear to be simple: the distal Rsp repeats are deleted in both Iso1ΔC8 and Iso1ΔC16 and the Iso1ΔC16Δ20 subline has further deletions of proximal Rsp repeats. The regions directly flanking the tandem Rsp repeats are largely unaltered in each subline. Fluorescence in situ hybridization (FISH) with Rsp probes and a control satellite not targeted by CRISPR (359-bp) in flies heterozygous for Iso1 and the deletion subline allele, confirm that the Rsp foci are demonstrably smaller in Iso1ΔC16 and Iso1ΔC16Δ20, consistent with their deletion sizes. The Iso1/Iso1 homozygote is the control. Arrows point to the Iso1 Rsp allele and arrowheads to the subline Rsp allele.