PMC5525351_01
Photomicrograph of N. lactamica Y92-1009. This image was obtained with transmission electron micrography and displays the diplococcoid nature of the N. lactamica Y92-1009 cell. The size of the cell is indicated in micrometres (mum)
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Fig1
An electron micrograph, generated by staining with a 1% potassium phosphotungstate (PTA) for 5-10 s and captured using a Philips EM300 with an accelerating voltage of 60 kV, is shown in Fig. 1.
Phylogenetic tree indicating the position of N. lactamica Y92-1009 amongst other pathogenic and commensal Neisseria. This tree was constructed based on a core genome comparison of a collection of 32 Neisseria assemblies generated using the genome comparator tool available on pubmlst.org/neisseria. The reconstructed evolutionary relationships among N. meningitidis (Red, n = 2), N. gonnorhoeae (Red, n = 1), N. cinerea (Yellow, n = 1) and N. lactamica (Black, n = 27) are shown. The genome sequenced here, N. lactamica Y92-1009 is outlined in cyan (Nla_PacBio|ST_3493). This analysis included the sequenced genome and the best representative assembly for every identified sequence type (ST) of this species. The tree was generated using FastTree v.2 and edited using Figtree v.1.4.3. The tree is drawn to scale, with branch length units being expressed as an overall proportion of divergence based on the comparison of 1629 genes
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Fig2
A core, gene by gene (n = 1629) MAAFT alignment of a collection of 32 whole genome Neisseria assemblies was done using the genome comparator tool available on Pubmlst.org/neisseria (Fig. 2).
Circular map of N. lactamica Y92-1009 genome and features generated with Cgview Comparison Tool. The arrows in the outermost ring indicate putative genes (with the arrow indicating the 5' to 3' direction on the positive strand.) identified and assigned to Clusters of Orthologous Groups (COGs). The 20 COG categories are indicated by different colours from Red to Grey according to the colour key. The second and third rings indicate regions containing coding sequence (Blue), tRNA (Orange), and other RNAs (Grey), with the second ring running 5' to 3' (positive strand) and the third ring running 3'to 5' (negative strand). The fourth ring indicates open reading frames assigned as COGs and encoded on the negative strand. The fifth, black, graph ring displays GC content while the last ring (purple and green) shows positive (Green) and negative (Purple) GC skew
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Fig3
Graphic showing phage related proteins identified in the intact prophage by PHAST. The diagram above was annotated by and imported from the PHAST-prophage database. Twenty-six hypothetical proteins were removed from the schematic to increase the clarity of the phage related proteins. The proteins above the black line indicating genome position are encoded 5' to 3' while the proteins under it are encoded 3' to 5'. The abbreviations in the diagrams are as follows Att (phage attachment site), Coa (Phage coat protein), fib (Phage Tail Fiber), Int (Phage integrase) Pla (Phage plate protein), PLP (Phage like protein), Por (Portal protein) sha (Phage tail shaft protein) Ter (Terminase)
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Fig4
These proteins include two attachment sites, two coat proteins, two tail-fiber proteins, an integrase, two plate, a portal, a tail shaft and terminase subunits (Fig. 4 ).