Fig 1.
Flowchart and visual output of PhasomeIt.
(A) Outputs of PhasomeIt can be viewed visually on the index page. Green bars indicate there is an homopolymeric tract within the open reading frame; orange bars indicate there is an SSR close to the gene of interest (for example in a promoter region); grey bars indicate there is a non-PV gene homologous to a PV gene in that same homology grouping; the remaining coloured bars are indicative of SSRs other than homopolymers which can be further derived from the dataset below the visual output. (B) Gene groupings corresponding to the visual output are found in a table below. From here, functions, PV status in each strain and tract entries can be obtained for the grouping of interest. The full dataset from which this figure is derived, containing further phasome information not discussed in this manuscript are available (https://figshare.com/s/d31b7b0b6ca4aeeb48df). A red outline shows highlights both the graphical and interactive outputs for the opa loci as an example.
Fig 2.
Range of phase variable genes identified in each species.
Data shown the median, range, upper and lower quartile number of PV genes, as indicated by presence of a repeat tract. These data exclude gene groupings which contain dinucleotide repeat tracts, due to the insufficient evidence of phase variation associated with dinucleotide repeats in the literature, and the loci discussed herein. Statistical analysis were performed with a Kruskal-Wallis test with Dunn’s multiple comparisons. NS; not significant, ***; p-value of <0.0005.
Table 1.
Variety of repeat types found in pathogenic and commensal Neisseria ssp.
Fig 3.
Tract length distribution in different Neisseria species.
Data are represented by heat maps. Colour intensity represents the percentage that a given tract length comprises of the total number of identified tracts of that type for each species. ‘-’ is indicative of no identified repeats of the given length. Information on the numbers of strains for each species, and numbers of tract lengths analysed can be found in Table 1.
Table 2.
Distribution of phase variable genes between phase variable modules.
Table 3.
Core phasome analysis of a subset of Neisseria species.
Table 4.
Exemplar gene groupings associated with in frame and read through phase variation.