Figure 3. A Genome-scale Screen Measures the Contribution of Each Parasite Gene to Fitness in Human Fibroblasts
(A) Diagram ofT. gondiichromosomes with genes colored according to phenotype.
(B and C) Significantly enriched (B) or depleted (C) gene sets identified by GSEA. Genes belonging to each category (gray) are plotted according to theirrank in the
screen, relative to the maximum enrichment score (red) and zero phenotype (green). Phenotype scores for a given set were compared to the entire set by a
Kolmogorov-Smirnov test (FDR corrected) to calculate thepvalues.
(D)T. gondiigenes rank-ordered based on their phenotype. Genes previously reported are highlighted, indicating whether they are dispensable (yellow), or
indispensable as inferred from overexpression (blue) or another method (red). Dotted line represents the median phenotype score for the dispensable genes.
Mean±SEM for n = 4 independent experiments. The two groups are compared in a box plot where whiskers indicate the most extreme data within 1.5 times the
interquartile range from the boxed quartiles (right).
(E) Correlation of phenotype scores to gene expression based on maximum RPKM values. The distribution of phenotypes in each expression quartile is plotted in
the violin graph. Bars indicate the group median.
(F) Analysis of selective pressure for 5,897 syntenic genes found in all three coccidian genomes (Tg,T. gondii;Nc,N. caninum;Hh,H. hammondi). Histogram
shows the distribution of dN/dSvalues, highlighting the top and bottom third. Genes binned according to dN/dSshow higher phenotype scores for genes under
purifying selection (orange). Bars indicate the group median. The distributions were compared using a Kolmogorov-Smirnov test.
(G) Correlation between phenotype scores and depth of conservation. The phylogenetic relationship betweenT. gondiiand the other genomes used in the
analysis is illustrated by the dendrogram, with number of genomes in each taxon indicated. The proportion ofT. gondiigenes and, within this, the proportion that
are functionally annotated, are shown for each category. The distribution of phenotype scores for each category is plotted. Bars indicate the group median.
See alsoFigures S1andS2andTables S1,S2, andS3.
Cell 167 , 1423–1435, September 8, 2016 1427