The general characteristics of the reference genomes are summarized in Table 3. The genome size ranged from 2 167 361 to 2 292 467 bp. The number of coding sequences (CDSs) after manual curation varied from 2295 to 2450 with an average CDS size of 796.6 bp. The number of core genes was 1820 and accessory genes ranged from 475 to 630. In Figure 1(a and b) BLAST atlases of the 14 reference genomes and all identified plasmid sequences, respectively, are displayed. Briefly, the reference genomes showed relatively high genomic similarity among all strains with the exception of two large insertions in WHO F and the presence or absence of the gonococcal genomic island (GGI).⁵⁸ The insertions in WHO F each include 34 almost identical predicted CDSs (31 984 bp) mainly containing an apparently complete type IV secretion system, a vapD virulence gene and xerC recombinase inserted into a tRNA-Asn element, with only weak matches to other sequences in the NCBI non-redundant nt database. Other regions with low genetic conservation corresponded to mobile genetic elements and prophages (Figure 1a).