Genome-wide screen controls and primary results.

(A) Plot of screen-wide controls’ effect on Wolbachia levels (Robust Z score normalized for each plate) included RNAi silencing of a host ribosomal gene RpL40 to increase Wolbachia, doxycycline treatment to decrease Wolbachia, RNAi silencing of Rho1 as a negative control, and RNAi silencing of a GFP-Jupiter transgene as a positive control for RNAi in our system that has no effect on Wolbachia levels. Bars represent the median and interquartile range of the robust Z scores for each control in the whole genome screen. (B) The whole genome screen yielded 1117 primary hits with a robust Z score of ≥1.5 or ≤-1.5. These genes included 329 genes that increase Wolbachia (magenta) and 788 genes that decrease Wolbachia (green) upon RNAi knockdown. (C) 1117 primary hits categorized according to confidence level (see S4 Fig). (D) 1117 primary hits’ effects on JW18 cell proliferation. For the genes that significantly increased Wolbachia levels (magenta), 12% (41 hits) significantly increased cell proliferation (robust Z > 1), 43% (141 hits) did not have a significant effect on cell proliferation, and 45% (147 hits) resulted in significant decreases in cell proliferation (robust Z< -1). For genes that significantly decreased Wolbachia levels (green), 2.4% (19 hits) significantly increased cell proliferation (robust Z > 1), 82% (644 hits) did not have a significant effect on cell proliferation, and 16% (125 hits) significantly decreased cell proliferation (robust Z < -1). See S4–S6 Figs for screening pipeline and further results analysis, S9 Fig for whole genome cell proliferation analysis, and S5 and S6 Tables for selection of amplicons and complete listing of genes.