Extended Data Fig. 2: Characteristics of the different essentialome classes.
From: A bacterial pan-genome makes gene essentiality strain-dependent and evolvable
a) Gene transcript abundance obtained by RNAseq collected from early exponential phase cultures of the 36 PG-collection strains growing in rich THY medium. Graph shows genes grouped by their essentialome classification. Black lines inside each plot represent the median, and dotted lines the first and third quartiles. p-values are obtained from a Tukey’s corrected one-way ANOVA. Results show that core universal, core strain-dependent and accessory essential genes tend to be more highly expressed compared to non-essential genes; b) Sequence diversity of S. pneumoniae genes split into the different essentialome classes and measured using the diameters of the clusters obtained by BF-Clust. Black lines inside each plot represent the median, and dotted lines the first and third quartiles. p-values are obtained from a Kruskal-Wallis test comparison. Strain-dependent versus accessory and non-essential classes presented the same p-value (<0.001). Results show that core universal and core strain-dependent essential genes are less genetically diverse than accessory and non-essential genes. The higher diversity in accessory essentials is at least partially caused by many of them being involved in ‘addiction-like’ systems, for example, systems consisting of two or more genes in which one of the genes is only required if the other/s are present (for example phage repressors, antitoxins from toxin-antitoxin systems, and methylases from restriction-modification systems). These genes may thus tolerate more mutations than a core genome gene involved in central processes, such as DNA replication; c) Functional categories enriched in Universal, Core Strain-dependent, and Accessory essentials. Each chart represents a COG category and the fraction of genes belonging to each essentialome class. Color coding is the same as previous panels. Asterisks indicate enrichments of essentialome class within COG category (adjusted p-value< 0.05). Analysis shows that universal essential genes are enriched in 5 central cellular processes categories, while core strain-dependent and accessory essentials are enriched for only two of these categories. The most enriched functional category of accessory essentials (cell wall, membrane and envelope biogenesis) can be explained by the high diversity of essential capsule type-specific biosynthesis genes.
