Fig. 1

Physical mapping and Hi-C scaffolding of the Culex quinquefasciatus genome. A The physical genome map. Numbers 1, 2, and 3 above the chromosomes stand for the chromosome numbers and letters p and q indicate chromosomal arms. Cytogenetic regions of the chromosomes are shown at the left side of the idiograms. Genomic coordinates in Mb are shown at the right side of the idiograms. B The crossing scheme to generate data by TrioCanu. Only M/m loci are shown, m1–m3 refer to possible variants in m sequences. The two parents were sequenced separately using Illumina. F1 males were sequenced by ONT. C A final Hi-C heat map for the Cx. quinquefasciatus genome. The position of the chromosomal inversion 3Rb is indicated by a rectangle. “Butterfly” shaped structure associated with inversion 3Rb is indicated by arrows. Centromere and breakpoint positions are shown by dashed lines. D An example of fluorescence in situ hybridization on mitotic chromosomes. Arrows indicate positions of the two BAC clones of interest. Hybridization of three other BAC clones is seen as red signals on 1q and 3q arms and blue signals on 2q arm. E Chromosome quotient (CQ). Each dot indicates a 1-kb fragment that showed a CQ value less than 0.05, indicating male specificity. Fragments with CQ values higher than 0.05 are not shown. The analysis was performed using repeat masked sequences and details are described in the “ Methods” section. F Fluorescence in situ hybridization of myoM gene and rDNA in chromosomes of male. Red and blue signals of the probes indicate location of the probes for myoM gene, a homolog of the Ae. aegypti M locus gene myo-sex, and rDNA, respectively