Fig. 5

Putative Fold-Back Regions (FBRs) and X’ Breakpoints further confirm accuracy of the X scaffold. A, B Polytene chromosome spreads demonstrating how the X and X’ chromosomes are usually found: folded back on itself with specific loci physically interacting. C Pictorial representation of what is known about the X and X’ chromosomes, FBRs, and inversion breakpoints. D Hi-C map from male pupae data showing three interacting loci and how they appear to correspond to the expected locations of FBRs along polytene maps. E Hi-C map from X’X adult female data [10] that shows the FBRs as well as two additional loci that correspond to the long paracentric inversion breakpoints. F An intermediate scatter plot heat map visualizing part of the long-range interaction peak cluster calling pipeline with squares demonstrating long-range interactions found by this method. G IGV Trace of the X chromosome with special attention to the locations identified as FBRs and breakpoints (top 3 tracks), as defined by our long-range Hi-C interaction peak detection method, and how they relate to repeat-rich and gene-rich regions. H Dot plot of extracted sequences corresponding to FBRs and breakpoint regions, showing sequence matches within and between each sequence. Blue dots represent matches on the same strand. Red dots represent matches on opposite strands. Polytene chromosome maps in C-E were reproduced from plates 1, 2 and 3 of Gabrusewycz-Garcia [31] with permission from Springer Nature under permission number: 5490830617309