Fig. 2
Chromosome identity, orientation, and assessment of the chromosome-scale scaffolds. A Interaction frequencies are visualized across Bcop_v1_corrected (Bcop_v1 after Hi-C guided correction), which was the input to Hi-C scaffolding. B Interaction frequencies visualized across the final version of Bcop_v2, after polytene orientation and with associated/unplaced contigs. Squares are drawn around boundaries of the four chromosome-scale scaffolds. C-F Anchoring, polytene map orientation, scaffold structural verification, and loci of interest on the chromosome-scale scaffolds for chromosomes (C) X, (D) II, (E) III, and (F) IV. The chromosome identity and specificity of each scaffold, their consistent orientations with polytene maps, and structural verifications were obtained using 10 unique “anchor” sequences with known chromosomal addresses mapped previously using in situ hybridization [17,18,19,20,21,22,23,24,25,26,27,28,29]. Centromeric sequences identified the expected locations of centromeres [22, 30,31,32] on acrocentric (X, II, and III) and meta-centric (IV) chromosomes, which were further supported by the density of a probe sequence (F4 from ScRTE) shown previously to be pericentromeric in all four chromosomes [32]. The scaffold for X also shows the locations found for the fold-back regions and long paracentric inversion breakpoints on the X’. Each chromosome-scale scaffold had at least one known unique sequence location anchoring it to a specific chromosome. There was no conflicting evidence with regard to chromosome identity nor with regard to the order in which sub-chromosomal sequences mapped along the scaffolds. Polytene chromosome maps were reproduced from plates 1, 2 and 3 of Gabrusewycz-Garcia [31] with permission from Springer Nature under permission number: 5490830617309. G Chromosome scaffold sizes are consistent with chromosome length expectations from Crouse [30]. H Chromosome scaffolds are consistent with read depth expectations on the X versus autosomes in males and females. Overall, this evidence suggests that Hi-C accurately ordered and oriented the contigs into chromosome-scale scaffolds corresponding to the expected four somatic chromosomes