Fig. 1: Pan-genome coverage and essential genes of Streptococcus pneumoniae PG collection.
From: A bacterial pan-genome makes gene essentiality strain-dependent and evolvable
a, Number of gene clusters belonging to the core and accessory genomes for the 208 strains study group determined by three different methods (PanX, BF-Clust and PPanGGOLiN). Orange represents how much of the accessory genome (>68%) is present in the PG collection. b, Number of genes called essential, non-essential, or uncertain across 21 strains, with mutant libraries ranked by saturation measured as the percentage of the total unique TA sites in the genome occupied by the ‘mariner’ transposon. c, Left: three representative genes showing the criteria used to classify genes as ‘universal’, ‘strain-dependent’ and ‘accessory essentials’. Each dot represents the essentiality score obtained for a gene in a specific strain. A score >0.9916 categorizes a gene as essential and <0.0424 as non-essential. Right: the number of genes assigned to each class. d, Distribution of fitness effects of non-essential and strain-dependent essentials in vitro in rich medium (SDMM) and in vivo in a mouse infection model (lungs)33. Black lines inside each plot represent the median, and dotted lines the first and third quartiles. P values were obtained from Tukey’s corrected one-way analysis of variance (ANOVA). e, Validation of gene essentiality. Transformation efficiency (TE) ratio is the ratio between the number of colony forming units (c.f.u.) obtained after transforming 1,000 ng of a PCR product targeting an essential gene and the c.f.u. obtained after transforming 1,000 ng of a PCR product that inserts into a neutral genomic region. TE ratios are shown for five universal and six strain-dependent essential genes in four different strain backgrounds. Experiments were performed in triplicate for each strain. Each dot in the panel represents a single strain’s experimental replicate. Black dots indicate strains where the targeted gene is non-essential, and red dots where the gene is essential. Squares indicate transformation experiments with successful knockout recovery.
