Comparison of copy number of the nuwts in homozygous and heterozygous fly lines and cured v. uncured flies. Cured (Panel A) and uncured (Panel B) Hawaii flies show the same correlation of qPCR results and sequencing coverage, although the qPCR results are shifted by the amplification of genes in the bacterial genome as they are plotted against the sequencing coverage obtained from the cured insects. This indicates that the duplication of the nuwt does not occur during the tetracycline treatment of the flies to compensate for the loss of the infection. The results of the qPCR assay for coverage was compared for homozygous cured Hawaii (Panels A) and the offspring of a Hawaii/Mexico cross which is heterozygous for the nuwt (Panels C) for the 3 kbp mate pair library library. Should the Hawaii line be heterozygous, the cross should have resulted in 50% of the offspring being homozygous for absence of single copy regions of the nuwt. Instead, each of the 44 offspring (half with Hawaii mothers and Mexico fathers and half from the reciprocal cross) tested positive by PCR for single copy genes in the nuwt and the nuwt was at half of the abundance of the Hawaii line relative to internal single copy Drosophila nuclear gene controls in 4 of these as seen by a shifting of the y-intercept by ~1 ΔCt.